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Tsaytler P, Blaess G, Scholze-Wittler M, Koch F, Herrmann BG. Early neural specification of stem cells is mediated by a set of SOX2-dependent neural-associated enhancers. Stem Cell Reports 2024:S2213-6711(24)00078-X. [PMID: 38579708 DOI: 10.1016/j.stemcr.2024.03.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
SOX2 is a transcription factor involved in the regulatory network maintaining the pluripotency of embryonic stem cells in culture as well as in early embryos. In addition, SOX2 plays a pivotal role in neural stem cell formation and neurogenesis. How SOX2 can serve both processes has remained elusive. Here, we identified a set of SOX2-dependent neural-associated enhancers required for neural lineage priming. They form a distinct subgroup (1,898) among 8,531 OCT4/SOX2/NANOG-bound enhancers characterized by enhanced SOX2 binding and chromatin accessibility. Activation of these enhancers is triggered by neural induction of wild-type cells or by default in Smad4-ablated cells resistant to mesoderm induction and is antagonized by mesodermal transcription factors via Sox2 repression. Our data provide mechanistic insight into the transition from the pluripotency state to the early neural fate and into the regulation of early neural versus mesodermal specification in embryonic stem cells and embryos.
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Affiliation(s)
- Pavel Tsaytler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Gaby Blaess
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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2
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Schifferl D, Scholze-Wittler M, Villaronga Luque A, Pustet M, Wittler L, Veenvliet JV, Koch F, Herrmann BG. Genome-wide identification of notochord enhancers comprising the regulatory landscape of the brachyury locus in mouse. Development 2023; 150:dev202111. [PMID: 37882764 PMCID: PMC10651091 DOI: 10.1242/dev.202111] [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: 06/22/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
The node and notochord are important signaling centers organizing the dorso-ventral patterning of cells arising from neuro-mesodermal progenitors forming the embryonic body anlage. Owing to the scarcity of notochord progenitors and notochord cells, a comprehensive identification of regulatory elements driving notochord-specific gene expression has been lacking. Here, we have used ATAC-seq analysis of FACS-purified notochord cells from Theiler stage 12-13 mouse embryos to identify 8921 putative notochord enhancers. In addition, we established a new model for generating notochord-like cells in culture, and found 3728 of these enhancers occupied by the essential notochord control factors brachyury (T) and/or Foxa2. We describe the regulatory landscape of the T locus, comprising ten putative enhancers occupied by these factors, and confirmed the regulatory activity of three of these elements. Moreover, we characterized seven new elements by knockout analysis in embryos and identified one new notochord enhancer, termed TNE2. TNE2 cooperates with TNE in the trunk notochord, and is essential for notochord differentiation in the tail. Our data reveal an essential role of Foxa2 in directing T-expressing cells towards the notochord lineage.
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Affiliation(s)
- Dennis Schifferl
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Alba Villaronga Luque
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Milena Pustet
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Frederic Koch
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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3
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Rogala S, Ali T, Melissari MT, Währisch S, Schuster P, Sarre A, Emídio RC, Boettger T, Rogg EM, Kaur J, Krishnan J, Dumbović G, Dimmeler S, Ounzain S, Pedrazzini T, Herrmann BG, Grote P. The lncRNA Sweetheart regulates compensatory cardiac hypertrophy after myocardial injury in murine males. Nat Commun 2023; 14:7024. [PMID: 37919291 PMCID: PMC10622434 DOI: 10.1038/s41467-023-42760-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
After myocardial infarction in the adult heart the remaining, non-infarcted tissue adapts to compensate the loss of functional tissue. This adaptation requires changes in gene expression networks, which are mostly controlled by transcription regulating proteins. Long non-coding transcripts (lncRNAs) are taking part in fine-tuning such gene programs. We describe and characterize the cardiomyocyte specific lncRNA Sweetheart RNA (Swhtr), an approximately 10 kb long transcript divergently expressed from the cardiac core transcription factor coding gene Nkx2-5. We show that Swhtr is dispensable for normal heart development and function but becomes essential for the tissue adaptation process after myocardial infarction in murine males. Re-expressing Swhtr from an exogenous locus rescues the Swhtr null phenotype. Genes that depend on Swhtr after cardiac stress are significantly occupied and therefore most likely regulated by NKX2-5. The Swhtr transcript interacts with NKX2-5 and disperses upon hypoxic stress in cardiomyocytes, indicating an auxiliary role of Swhtr for NKX2-5 function in tissue adaptation after myocardial injury.
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Affiliation(s)
- Sandra Rogala
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, 60596, Frankfurt am Main, Germany
| | - Tamer Ali
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, 60596, Frankfurt am Main, Germany
- Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Maria-Theodora Melissari
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sandra Währisch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany
| | - Peggy Schuster
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne Medical School, Lausanne, Switzerland
| | - Rebeca Cordellini Emídio
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas Boettger
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, 61231, Bad Nauheim, Germany
| | - Eva-Maria Rogg
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Jaskiran Kaur
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Jaya Krishnan
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Gabrijela Dumbović
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Samir Ounzain
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- HAYA Therapeutics, Rte de la Corniche 6, 1066, Lausanne, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, 60596, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany.
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4
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Tsaytler P, Liu J, Blaess G, Schifferl D, Veenvliet JV, Wittler L, Timmermann B, Herrmann BG, Koch F. BMP4 triggers regulatory circuits specifying the cardiac mesoderm lineage. Development 2023; 150:310518. [PMID: 37082965 DOI: 10.1242/dev.201450] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
Cardiac lineage specification in the mouse is controlled by TGFβ and WNT signaling. From fly to fish, BMP has been identified as indispensable heart inducer. A detailed analysis of the role of Bmp4 and its effectors Smad1/5, however, were still missing. We show that Bmp4 induces cardiac mesoderm formation in murine ESCs in vitro. Bmp4 first activates Wnt3 and up-regulates Nodal. pSmad1/5 and the WNT effector Tcf3 form a complex, and together with pSmad2/3 activate mesoderm enhancers and Eomes. They then cooperate with Eomes to consolidate the expression of many mesoderm factors, including T. Eomes and T form a positive feedback loop and open additional enhancers regulating early mesoderm genes, including the transcription factor Mesp1 establishing the cardiac mesoderm lineage. In parallel the neural fate is suppressed. Our data confirm the pivotal role of Bmp4 in cardiac mesoderm formation in the mouse. We describe in detail the consecutive and cooperative actions of three signaling pathways, BMP, WNT and Nodal, and their effector transcription factors, during cardiac mesoderm specification.
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Affiliation(s)
- Pavel Tsaytler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Jinhua Liu
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Gaby Blaess
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Dennis Schifferl
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
| | - Frederic Koch
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
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5
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Gehlen J, Giel AS, Köllges R, Haas SL, Zhang R, Trcka J, Sungur AÖ, Renziehausen F, Bornholdt D, Jung D, Hoyer PD, Nordenskjöld A, Tibboel D, Vlot J, Spaander MC, Smigiel R, Patkowski D, Roeleveld N, van Rooij IALM, de Blaauw I, Hölscher A, Pauly M, Leutner A, Fuchs J, Niethammer J, Melissari MT, Jenetzky E, Zwink N, Thiele H, Hilger AC, Hess T, Trautmann J, Marks M, Baumgarten M, Bläss G, Landén M, Fundin B, Bulik CM, Pennimpede T, Ludwig M, Ludwig KU, Mangold E, Heilmann-Heimbach S, Moebus S, Herrmann BG, Alsabeah K, Burgos CM, Lilja HE, Azodi S, Stenström P, Arnbjörnsson E, Frybova B, Lebensztejn DM, Debek W, Kolodziejczyk E, Kozera K, Kierkus J, Kaliciński P, Stefanowicz M, Socha-Banasiak A, Kolejwa M, Piaseczna-Piotrowska A, Czkwianianc E, Nöthen MM, Grote P, Rygl M, Reinshagen K, Spychalski N, Ludwikowski B, Hubertus J, Heydweiller A, Ure B, Muensterer OJ, Aubert O, Gosemann JH, Lacher M, Degenhardt P, Boemers TM, Mokrowiecka A, Małecka-Panas E, Wöhr M, Knapp M, Seitz G, de Klein A, Oracz G, Brosens E, Reutter H, Schumacher J. First genome-wide association study of esophageal atresia with or without tracheoesophageal fistula (EA/TEF) identifies three genetic risk loci at CTNNA3, FOXF1/FOXC2/FOXL1 and HNF1B. Human Genetics and Genomics Advances 2022; 3:100093. [PMID: 35199045 PMCID: PMC8844277 DOI: 10.1016/j.xhgg.2022.100093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
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6
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Schifferl D, Scholze-Wittler M, Wittler L, Veenvliet JV, Koch F, Herrmann BG. A 37 kb region upstream of brachyury comprising a notochord enhancer is essential for notochord and tail development. Development 2021; 148:273520. [PMID: 34822716 PMCID: PMC8722351 DOI: 10.1242/dev.200059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
The node-streak border region comprising notochord progenitor cells (NPCs) at the posterior node and neuro-mesodermal progenitor cells (NMPs) in the adjacent epiblast is the prime organizing center for axial elongation in mouse embryos. The T-box transcription factor brachyury (T) is essential for both formation of the notochord and maintenance of NMPs, and thus is a key regulator of trunk and tail development. The T promoter controlling T expression in NMPs and nascent mesoderm has been characterized in detail; however, control elements for T expression in the notochord have not been identified yet. We have generated a series of deletion alleles by CRISPR/Cas9 genome editing in mESCs, and analyzed their effects in mutant mouse embryos. We identified a 37 kb region upstream of T that is essential for notochord function and tailbud outgrowth. Within that region, we discovered a T-binding enhancer required for notochord cell specification and differentiation. Our data reveal a complex regulatory landscape controlling cell type-specific expression and function of T in NMP/nascent mesoderm and node/notochord, allowing proper trunk and tail development. Summary: Genetic dissection of the mouse brachyury locus identifies a notochord enhancer and predicts additional control elements essential for trunk and tail development of the mouse embryo.
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Affiliation(s)
- Dennis Schifferl
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.,Institute of Biology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Frederic Koch
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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7
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Bolondi A, Haut L, Gassaloglu SI, Burton P, Kretzmer H, Buschow R, Meissner A, Herrmann BG, Veenvliet JV. Generation of Mouse Pluripotent Stem Cell-derived Trunk-like Structures: An in vitro Model of Post-implantation Embryogenesis. Bio Protoc 2021; 11:e4042. [PMID: 34250208 PMCID: PMC8250383 DOI: 10.21769/bioprotoc.4042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 11/02/2022] Open
Abstract
Post-implantation mammalian embryogenesis involves profound molecular, cellular, and morphogenetic changes. The study of these highly dynamic processes is complicated by the limited accessibility of in utero development. In recent years, several complementary in vitro systems comprising self-organized assemblies of mouse embryonic stem cells, such as gastruloids, have been reported. We recently demonstrated that the morphogenetic potential of gastruloids can be further unlocked by the addition of a low percentage of Matrigel as an extracellular matrix surrogate. This resulted in the formation of highly organized trunk-like structures (TLSs) with a neural tube that is frequently flanked by bilateral somites. Notably, development at the molecular and morphogenetic levels is highly reminiscent of the natural embryo. To facilitate access to this powerful model, here we provide a detailed step-by-step protocol that should allow any lab with access to standard cell culture techniques to implement the culture system. This will provide the user with a means to investigate early mid-gestational mouse embryogenesis at an unprecedented spatiotemporal resolution.
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Affiliation(s)
- Adriano Bolondi
- Dept. of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Leah Haut
- Dept. of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Polly Burton
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Helene Kretzmer
- Dept. of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - René Buschow
- Microscopy and Cryo-Electron Microscopy, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Alexander Meissner
- Dept. of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bernhard G. Herrmann
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical Genetics, Charité - University Medicine Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Jesse V. Veenvliet
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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8
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Veenvliet JV, Bolondi A, Kretzmer H, Haut L, Scholze-Wittler M, Schifferl D, Koch F, Guignard L, Kumar AS, Pustet M, Heimann S, Buschow R, Wittler L, Timmermann B, Meissner A, Herrmann BG. Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites. Science 2021; 370:370/6522/eaba4937. [PMID: 33303587 DOI: 10.1126/science.aba4937] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/13/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022]
Abstract
Post-implantation embryogenesis is a highly dynamic process comprising multiple lineage decisions and morphogenetic changes that are inaccessible to deep analysis in vivo. We found that pluripotent mouse embryonic stem cells (mESCs) form aggregates that upon embedding in an extracellular matrix compound induce the formation of highly organized "trunk-like structures" (TLSs) comprising the neural tube and somites. Comparative single-cell RNA sequencing analysis confirmed that this process is highly analogous to mouse development and follows the same stepwise gene-regulatory program. Tbx6 knockout TLSs developed additional neural tubes mirroring the embryonic mutant phenotype, and chemical modulation could induce excess somite formation. TLSs thus reveal an advanced level of self-organization and provide a powerful platform for investigating post-implantation embryogenesis in a dish.
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Affiliation(s)
- Jesse V Veenvliet
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Leah Haut
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dennis Schifferl
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Léo Guignard
- Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, 10115 Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Milena Pustet
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Simon Heimann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - René Buschow
- Microscopy and Cryo-Electron Microscopy, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. .,Institute for Medical Genetics, Charité-University Medicine Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
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9
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Abstract
Mammalian post-implantation development comprises the coordination of complex lineage decisions and morphogenetic processes shaping the embryo. Despite technological advances, a comprehensive understanding of the dynamics of these processes and of the self-organization capabilities of stem cells and their descendants remains elusive. Building synthetic embryo-like structures from pluripotent embryonic stem cells in vitro promises to fill these knowledge gaps and thereby may prove transformative for developmental biology. Initial efforts to model the post-implantation embryo resulted in structures with compromised morphology (gastruloids). Recent approaches employing modified culture media, an extracellular matrix surrogate or extra-embryonic stem cells, however, succeeded in establishing embryo-like architecture. For example, embedding of gastruloids in Matrigel unlocked self-organization into trunk-like structures with bilateral somites and a neural tube-like structure, together with gut tissue and primordial germ cell-like cells. In this review, we describe the currently available models, discuss how these can be employed to acquire novel biological insights, and detail the imminent challenges for improving current models by in vitro engineering.
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Affiliation(s)
- Jesse V Veenvliet
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Bernhard G Herrmann
- Dept. of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany; Institute for Medical Genetics, Charité - University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203, Berlin, Germany.
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10
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Veenvliet JV, Bolondi A, Kretzmer H, Haut L, Scholze-Wittler M, Schifferl D, Koch F, Guignard L, Kumar AS, Pustet M, Heimann S, Buschow R, Wittler L, Timmermann B, Meissner A, Herrmann BG. Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites. Science 2020. [PMID: 33303587 DOI: 10.1101/2020.1103.1104.974949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Post-implantation embryogenesis is a highly dynamic process comprising multiple lineage decisions and morphogenetic changes that are inaccessible to deep analysis in vivo. We found that pluripotent mouse embryonic stem cells (mESCs) form aggregates that upon embedding in an extracellular matrix compound induce the formation of highly organized "trunk-like structures" (TLSs) comprising the neural tube and somites. Comparative single-cell RNA sequencing analysis confirmed that this process is highly analogous to mouse development and follows the same stepwise gene-regulatory program. Tbx6 knockout TLSs developed additional neural tubes mirroring the embryonic mutant phenotype, and chemical modulation could induce excess somite formation. TLSs thus reveal an advanced level of self-organization and provide a powerful platform for investigating post-implantation embryogenesis in a dish.
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Affiliation(s)
- Jesse V Veenvliet
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Leah Haut
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dennis Schifferl
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Léo Guignard
- Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, 10115 Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Milena Pustet
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Simon Heimann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - René Buschow
- Microscopy and Cryo-Electron Microscopy, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
- Institute for Medical Genetics, Charité-University Medicine Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
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11
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Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [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] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
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Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
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12
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Charron Y, Willert J, Lipkowitz B, Kusecek B, Herrmann BG, Bauer H. Two isoforms of the RAC-specific guanine nucleotide exchange factor TIAM2 act oppositely on transmission ratio distortion by the mouse t-haplotype. PLoS Genet 2019; 15:e1007964. [PMID: 30817801 PMCID: PMC6394906 DOI: 10.1371/journal.pgen.1007964] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 03/29/2018] [Accepted: 01/15/2019] [Indexed: 11/18/2022] Open
Abstract
Transmission ratio distortion (TRD) by the mouse t-haplotype, a variant region on chromosome 17, is a well-studied model of non-Mendelian inheritance. It is characterized by the high transmission ratio (up to 99%) of the t-haplotype from t/+ males to their offspring. TRD is achieved by the exquisite ability of the responder (Tcr) to trigger non-Mendelian inheritance of homologous chromosomes. Several distorters (Tcd1-Tcd4), which act cumulatively, together promote the high transmission ratio of Tcr and the t-haplotype. Molecularly, TRD is brought about by deregulation of Rho signaling pathways via the distorter products, which impair sperm motility, and the t-sperm specific rescue of sperm motility by the responder. The t-sperm thus can reach the egg cells faster than +-sperm and fertilize them. Previously we have shown that the responder function is accomplished by a dominant negative form of sperm motility kinase (SMOKTCR), while the distorter functions are accomplished by the Rho G protein regulators TAGAP, FGD2 and NME3 proposed to function in two oppositely acting pathways. Here we identify the RAC1-specific guanine nucleotide exchange factor TIAM2 as modifier of t-haplotype TRD. Tiam2 is expressed in two isoforms, the full-length (Tiam2l) and a short transcript (Tiam2s). Tiam2s expression from the t-allele is strongly increased compared to the wild-type allele. By transgenic approaches we show that Tiam2s enhances t-haplotype transmission, while Tiam2l has the opposite effect. Our data show that a single modifier locus can encode different gene products exerting opposite effects on a trait. They also suggest that the expression ratio of the isoforms determines if the outcome is an enhancing or a suppressive effect on the trait.
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Affiliation(s)
- Yves Charron
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for medical Genetics, Campus Benjamin-Franklin, Charité –University Medicine Berlin, Berlin, Germany
| | - Jürgen Willert
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bettina Lipkowitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Barica Kusecek
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for medical Genetics, Campus Benjamin-Franklin, Charité –University Medicine Berlin, Berlin, Germany
- * E-mail: (BGH); (HB)
| | - Hermann Bauer
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (BGH); (HB)
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13
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Weitensteiner V, Zhang R, Bungenberg J, Marks M, Gehlen J, Ralser DJ, Hilger AC, Sharma A, Schumacher J, Gembruch U, Merz WM, Becker A, Altmüller J, Thiele H, Herrmann BG, Odermatt B, Ludwig M, Reutter H. Exome sequencing in syndromic brain malformations identifies novel mutations in ACTB, and SLC9A6, and suggests BAZ1A as a new candidate gene. Birth Defects Res 2018; 110:587-597. [PMID: 29388391 DOI: 10.1002/bdr2.1200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 10/31/2017] [Revised: 12/07/2017] [Accepted: 01/06/2018] [Indexed: 02/01/2023]
Abstract
BACKGROUND Syndromic brain malformations comprise a large group of anomalies with a birth prevalence of about 1 in 1,000 live births. Their etiological factors remain largely unknown. To identify causative mutations, we used whole-exome sequencing (WES) in aborted fetuses and children with syndromic brain malformations in which chromosomal microarray analysis was previously unremarkable. METHODS WES analysis was applied in eight case-parent trios, six aborted fetuses, and two children. RESULTS WES identified a novel de novo mutation (p.Gly268Arg) in ACTB (Baraitser-Winter syndrome-1), a homozygous stop mutation (p.R2442*) in ASPM (primary microcephaly type 5), and a novel hemizygous X-chromosomal mutation (p.I250V) in SLC9A6 (X-linked syndromic mentaly retardation, Christianson type). Furthermore, WES identified a de novo mutation (p.Arg1093Gln) in BAZ1A. This mutation was previously reported in only one allele in 121.362 alleles tested (dbSNP build 147). BAZ1A has been associated with neurodevelopmental impairment and dysregulation of several pathways including vitamin D metabolism. Here, serum vitamin-D (25-(OH)D) levels were insufficient and gene expression comparison between the child and her parents identified 27 differentially expressed genes. Of note, 10 out of these 27 genes are associated to cytoskeleton, integrin and synaptic related pathways, pinpointing to the relevance of BAZ1A in neural development. In situ hybridization in mouse embryos between E10.5 and E13.5 detected Baz1a expression in the central and peripheral nervous system. CONCLUSION In syndromic brain malformations, WES is likely to identify causative mutations when chromosomal microarray analysis is unremarkable. Our findings suggest BAZ1A as a possible new candidate gene.
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Affiliation(s)
- Valerie Weitensteiner
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany
| | - Rong Zhang
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany.,Department of Genomics-Life & Brain Center, Bonn, Germany
| | | | - Matthias Marks
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Jan Gehlen
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany.,Department of Genomics-Life & Brain Center, Bonn, Germany
| | - Damian J Ralser
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany.,Department of Pediatrics, University of Bonn, Bonn, Germany
| | - Amit Sharma
- Department of Neurology, University Clinic Bonn, Bonn, Germany
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany.,Department of Genomics-Life & Brain Center, Bonn, Germany
| | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn, Germany
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn School of Medicine and University Hospital of Bonn, Bonn, Germany.,Department of Genomics-Life & Brain Center, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
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14
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Beisaw A, Tsaytler P, Koch F, Schmitz SU, Melissari MT, Senft AD, Wittler L, Pennimpede T, Macura K, Herrmann BG, Grote P. BRACHYURY directs histone acetylation to target loci during mesoderm development. EMBO Rep 2017; 19:118-134. [PMID: 29141987 DOI: 10.15252/embr.201744201] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/19/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022] Open
Abstract
T-box transcription factors play essential roles in multiple aspects of vertebrate development. Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. A single point mutation (TY88A) results in decreased histone 3 lysine 27 acetylation (H3K27ac) at T target sites, including the T locus, suggesting that T autoregulates the maintenance of its expression and functions by recruiting permissive chromatin modifications to putative enhancers during mesoderm specification. Our data indicate that T mediates H3K27ac recruitment through a physical interaction with p300. In addition, we determine that T plays a prominent role in the specification of hematopoietic and endothelial cell types. Hematopoietic and endothelial gene expression programs are disrupted in TY88A mutant embryos, leading to a defect in the differentiation of hematopoietic progenitors. We show that this role of T is mediated, at least in part, through activation of a distal Lmo2 enhancer.
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Affiliation(s)
- Arica Beisaw
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.,Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Pavel Tsaytler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria-Theodora Melissari
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna D Senft
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Karol Macura
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical Genetics, Charité-University Medicine Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany .,Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
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15
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Lange L, Marks M, Liu J, Wittler L, Bauer H, Piehl S, Bläß G, Timmermann B, Herrmann BG. Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a. Biol Open 2017; 6:752-764. [PMID: 28619992 PMCID: PMC5483016 DOI: 10.1242/bio.023200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mouse t haplotype, a variant 20 cM genomic region on Chromosome 17, harbors 16 embryonic control genes identified by recessive lethal mutations isolated from wild mouse populations. Due to technical constraints so far only one of these, the tw5 lethal, has been cloned and molecularly characterized. Here we report the molecular isolation of the tw18 lethal. Embryos carrying the tw18 lethal die from major gastrulation defects commencing with primitive streak formation at E6.5. We have used transcriptome and marker gene analyses to describe the molecular etiology of the tw18 phenotype. We show that both WNT and Nodal signal transduction are impaired in the mutant epiblast, causing embryonic patterning defects and failure of primitive streak and mesoderm formation. By using a candidate gene approach, gene knockout by homologous recombination and genetic rescue, we have identified the gene causing the tw18 phenotype as Ppp2r1a, encoding the PP2A scaffolding subunit PR65alpha. Our work highlights the importance of phosphatase 2A in embryonic patterning, primitive streak formation, gastrulation, and mesoderm formation downstream of WNT and Nodal signaling.
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Affiliation(s)
- Lisette Lange
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany.,Free University Berlin, Department of Biology, Chemistry and Pharmacy, Takustrasse 3, Berlin 14195, Germany
| | - Matthias Marks
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Jinhua Liu
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Hermann Bauer
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Sandra Piehl
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Gabriele Bläß
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, Berlin 14195, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestraße 63-73, Berlin 14195, Germany .,Charité-University Medicine Berlin, Institute for Medical Genetics, Campus Benjamin Franklin, Hindenburgdamm 30, Berlin 12203, Germany
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16
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Riemer P, Rydenfelt M, Marks M, van Eunen K, Thedieck K, Herrmann BG, Blüthgen N, Sers C, Morkel M. Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids. J Cell Biol 2017; 216:1567-1577. [PMID: 28442534 PMCID: PMC5461020 DOI: 10.1083/jcb.201610058] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 10/18/2016] [Revised: 02/08/2017] [Accepted: 03/30/2017] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer is driven by cooperating oncogenic mutations. In this study, we use organotypic cultures derived from transgenic mice inducibly expressing oncogenic β-catenin and/or PIK3CAH1047R to follow sequential changes in cancer-related signaling networks, intestinal cell metabolism, and physiology in a three-dimensional environment mimicking tissue architecture. Activation of β-catenin alone results in the formation of highly clonogenic cells that are nonmotile and prone to undergo apoptosis. In contrast, coexpression of stabilized β-catenin and PIK3CAH1047R gives rise to intestinal cells that are apoptosis-resistant, proliferative, stem cell-like, and motile. Systematic inhibitor treatments of organoids followed by quantitative phenotyping and phosphoprotein analyses uncover key changes in the signaling network topology of intestinal cells after induction of stabilized β-catenin and PIK3CAH1047R We find that survival and motility of organoid cells are associated with 4EBP1 and AKT phosphorylation, respectively. Our work defines phenotypes, signaling network states, and vulnerabilities of transgenic intestinal organoids as a novel approach to understanding oncogene activities and guiding the development of targeted therapies.
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Affiliation(s)
- Pamela Riemer
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Mattias Rydenfelt
- Integrative Research Institute Life Sciences, Humboldt University Berlin, 10099 Berlin, Germany
| | - Matthias Marks
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Karen van Eunen
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Kathrin Thedieck
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Nils Blüthgen
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,Integrative Research Institute Life Sciences, Humboldt University Berlin, 10099 Berlin, Germany
| | - Christine Sers
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Markus Morkel
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
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17
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Sudheer S, Liu J, Marks M, Koch F, Anurin A, Scholze M, Senft AD, Wittler L, Macura K, Grote P, Herrmann BG. Different Concentrations of FGF Ligands, FGF2 or FGF8 Determine Distinct States of WNT-Induced Presomitic Mesoderm. Stem Cells 2016; 34:1790-800. [DOI: 10.1002/stem.2371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 02/07/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Smita Sudheer
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU; United Kingdom
| | - Jinhua Liu
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Matthias Marks
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Frederic Koch
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Anna Anurin
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Department of Biology; Chemistry and Pharmacy, Free University Berlin; Berlin Germany
| | - Manuela Scholze
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Anna Dorothea Senft
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE; United Kingdom
| | - Lars Wittler
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Karol Macura
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Phillip Grote
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main; Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
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18
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Schmitz SU, Grote P, Herrmann BG. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 2016; 73:2491-509. [PMID: 27007508 PMCID: PMC4894931 DOI: 10.1007/s00018-016-2174-5] [Citation(s) in RCA: 729] [Impact Index Per Article: 91.1] [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: 02/01/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Since decades it has been known that non-protein-coding RNAs have important cellular functions. Deep sequencing recently facilitated the discovery of thousands of novel transcripts, now classified as long noncoding RNAs (lncRNAs), in many vertebrate and invertebrate species. LncRNAs are involved in a wide range of cellular mechanisms, from almost all aspects of gene expression to protein translation and stability. Recent findings implicate lncRNAs as key players of cellular differentiation, cell lineage choice, organogenesis and tissue homeostasis. Moreover, lncRNAs are involved in pathological conditions such as cancer and cardiovascular disease, and therefore provide novel biomarkers and pharmaceutical targets. Here we discuss examples illustrating the versatility of lncRNAs in gene control, development and differentiation, as well as in human disease.
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Affiliation(s)
- Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany. .,Institute for Medical Genetics, Campus Benjamin Franklin, Charite-University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
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19
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Hwang DY, Kohl S, Fan X, Vivante A, Chan S, Dworschak GC, Schulz J, van Eerde AM, Hilger AC, Gee HY, Pennimpede T, Herrmann BG, van de Hoek G, Renkema KY, Schell C, Huber TB, Reutter HM, Soliman NA, Stajic N, Bogdanovic R, Kehinde EO, Lifton RP, Tasic V, Lu W, Hildebrandt F. Mutations of the SLIT2-ROBO2 pathway genes SLIT2 and SRGAP1 confer risk for congenital anomalies of the kidney and urinary tract. Hum Genet 2015; 134:905-16. [PMID: 26026792 PMCID: PMC4497857 DOI: 10.1007/s00439-015-1570-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [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: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 12/26/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) account for 40-50% of chronic kidney disease that manifests in the first two decades of life. Thus far, 31 monogenic causes of isolated CAKUT have been described, explaining ~12% of cases. To identify additional CAKUT-causing genes, we performed whole-exome sequencing followed by a genetic burden analysis in 26 genetically unsolved families with CAKUT. We identified two heterozygous mutations in SRGAP1 in 2 unrelated families. SRGAP1 is a small GTPase-activating protein in the SLIT2-ROBO2 signaling pathway, which is essential for development of the metanephric kidney. We then examined the pathway-derived candidate gene SLIT2 for mutations in cohort of 749 individuals with CAKUT and we identified 3 unrelated individuals with heterozygous mutations. The clinical phenotypes of individuals with mutations in SLIT2 or SRGAP1 were cystic dysplastic kidneys, unilateral renal agenesis, and duplicated collecting system. We show that SRGAP1 is expressed in early mouse nephrogenic mesenchyme and that it is coexpressed with ROBO2 in SIX2-positive nephron progenitor cells of the cap mesenchyme in developing rat kidney. We demonstrate that the newly identified mutations in SRGAP1 lead to an augmented inhibition of RAC1 in cultured human embryonic kidney cells and that the SLIT2 mutations compromise the ability of the SLIT2 ligand to inhibit cell migration. Thus, we report on two novel candidate genes for causing monogenic isolated CAKUT in humans.
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Affiliation(s)
- Daw-Yang Hwang
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Stefan Kohl
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xueping Fan
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stefanie Chan
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Gabriel C Dworschak
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julian Schulz
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Albertien M van Eerde
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tracie Pennimpede
- Max Planck Institute for Molecular Genetics, Developmental Genetics Department, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Developmental Genetics Department, Berlin, Germany
| | - Glenn van de Hoek
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kirsten Y Renkema
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christoph Schell
- Renal Division, University Hospital Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Tobias B Huber
- Renal Division, University Hospital Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Germany
| | - Heiko M Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Neonatology, Children’s Hospital, University of Bonn, Bonn, Germany
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
- Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Natasa Stajic
- Medical Faculty, University of Belgrade, Belgrade, Serbia
- Institute of Mother and Child Healthcare of Serbia, Belgrade, Serbia
| | - Radovan Bogdanovic
- Medical Faculty, University of Belgrade, Belgrade, Serbia
- Institute of Mother and Child Healthcare of Serbia, Belgrade, Serbia
| | | | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children’s Hospital, Skopje, Macedonia
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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20
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Grote P, Herrmann BG. Long noncoding RNAs in organogenesis: making the difference. Trends Genet 2015; 31:329-35. [DOI: 10.1016/j.tig.2015.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 01/06/2023]
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21
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Draaken M, Knapp M, Pennimpede T, Schmidt JM, Ebert AK, Rösch W, Stein R, Utsch B, Hirsch K, Boemers TM, Mangold E, Heilmann S, Ludwig KU, Jenetzky E, Zwink N, Moebus S, Herrmann BG, Mattheisen M, Nöthen MM, Ludwig M, Reutter H. Genome-wide association study and meta-analysis identify ISL1 as genome-wide significant susceptibility gene for bladder exstrophy. PLoS Genet 2015; 11:e1005024. [PMID: 25763902 PMCID: PMC4357422 DOI: 10.1371/journal.pgen.1005024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [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: 08/20/2014] [Accepted: 01/26/2015] [Indexed: 11/18/2022] Open
Abstract
The bladder exstrophy-epispadias complex (BEEC) represents the severe end of the uro-rectal malformation spectrum, and is thought to result from aberrant embryonic morphogenesis of the cloacal membrane and the urorectal septum. The most common form of BEEC is isolated classic bladder exstrophy (CBE). To identify susceptibility loci for CBE, we performed a genome-wide association study (GWAS) of 110 CBE patients and 1,177 controls of European origin. Here, an association was found with a region of approximately 220kb on chromosome 5q11.1. This region harbors the ISL1 (ISL LIM homeobox 1) gene. Multiple markers in this region showed evidence for association with CBE, including 84 markers with genome-wide significance. We then performed a meta-analysis using data from a previous GWAS by our group of 98 CBE patients and 526 controls of European origin. This meta-analysis also implicated the 5q11.1 locus in CBE risk. A total of 138 markers at this locus reached genome-wide significance in the meta-analysis, and the most significant marker (rs9291768) achieved a P value of 2.13 × 10-12. No other locus in the meta-analysis achieved genome-wide significance. We then performed murine expression analyses to follow up this finding. Here, Isl1 expression was detected in the genital region within the critical time frame for human CBE development. Genital regions with Isl1 expression included the peri-cloacal mesenchyme and the urorectal septum. The present study identified the first genome-wide significant locus for CBE at chromosomal region 5q11.1, and provides strong evidence for the hypothesis that ISL1 is the responsible candidate gene in this region.
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Affiliation(s)
- Markus Draaken
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- * E-mail:
| | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
- * E-mail:
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
| | | | - Anne-Karolin Ebert
- Department of Urology and Pediatric Urology, University Hospital of Ulm, Germany
| | - Wolfgang Rösch
- Department of Pediatric Urology, St. Hedwig Hospital Barmherzige Brüder, Regensburg, Germany
| | - Raimund Stein
- Department of Urology, Division of Pediatric Urology, University of Mainz, Mainz, Germany
| | - Boris Utsch
- Department of General Pediatrics and Neonatology, Justus Liebig University, Giessen, Germany
| | - Karin Hirsch
- Department of Urology, Division of Paediatric Urology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas M. Boemers
- Department of Pediatric Surgery and Pediatric Urology, Children’s Hospital of Cologne, Cologne, Germany
| | | | - Stefanie Heilmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Ekkehart Jenetzky
- Department of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, Johannes-Gutenberg University, Mainz, Germany
| | - Nadine Zwink
- Department of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry, and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Manuel Mattheisen
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
- * E-mail:
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22
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Schwartz B, Marks M, Wittler L, Werber M, Währisch S, Nordheim A, Herrmann BG, Grote P. SRF is essential for mesodermal cell migration during elongation of the embryonic body axis. Mech Dev 2014; 133:23-35. [PMID: 25020278 DOI: 10.1016/j.mod.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 09/24/2013] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 12/22/2022]
Abstract
Mesoderm formation in the mouse embryo initiates around E6.5 at the primitive streak and continues until the end of axis extension at E12.5. It requires the process of epithelial-to-mesenchymal transition (EMT), wherein cells detach from the epithelium, adopt mesenchymal cell morphology, and gain competence to migrate. It was shown previously that, prior to mesoderm formation, the transcription factor SRF (Serum Response Factor) is essential for the formation of the primitive streak. To elucidate the role of murine Srf in mesoderm formation during axis extension we conditionally inactivated Srf in nascent mesoderm using the T(s)::Cre driver mouse. Defects in mutant embryos became apparent at E8.75 in the heart and in the allantois. From E9.0 onwards body axis elongation was arrested. Using genome-wide expression analysis, combined with SRF occupancy data from ChIP-seq analysis, we identified a set of direct SRF target genes acting in posterior nascent mesoderm which are enriched for transcripts associated with migratory function. We further show that cell migration is impaired in Srf mutant embryos. Thus, the primary role for SRF in the nascent mesoderm during elongation of the embryonic body axis is the activation of a migratory program, which is a prerequisite for axis extension.
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Affiliation(s)
- Benedikt Schwartz
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Free University Berlin, Dept. of Biology, Chemistry and Pharmacy, Takustrasse 3, 14195 Berlin, Germany
| | - Matthias Marks
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Martin Werber
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Sandra Währisch
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Alfred Nordheim
- Department of Molecular Biology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Phillip Grote
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
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23
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Reutter H, Draaken M, Pennimpede T, Wittler L, Brockschmidt FF, Ebert AK, Bartels E, Rösch W, Boemers TM, Hirsch K, Schmiedeke E, Meesters C, Becker T, Stein R, Utsch B, Mangold E, Nordenskjöld A, Barker G, Kockum CC, Zwink N, Holmdahl G, Läckgren G, Jenetzky E, Feitz WFJ, Marcelis C, Wijers CHW, Van Rooij IALM, Gearhart JP, Herrmann BG, Ludwig M, Boyadjiev SA, Nöthen MM, Mattheisen M. Genome-wide association study and mouse expression data identify a highly conserved 32 kb intergenic region between WNT3 and WNT9b as possible susceptibility locus for isolated classic exstrophy of the bladder. Hum Mol Genet 2014; 23:5536-44. [PMID: 24852367 DOI: 10.1093/hmg/ddu259] [Citation(s) in RCA: 17] [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: 11/12/2022] Open
Abstract
Bladder exstrophy-epispadias complex (BEEC), the severe end of the urorectal malformation spectrum, has a profound impact on continence as well as sexual and renal functions. It is widely accepted that for the majority of cases the genetic basis appears to be multifactorial. Here, we report the first study which utilizes genome-wide association methods to analyze a cohort comprising patients presenting the most common BEEC form, classic bladder exstrophy (CBE), to identify common variation associated with risk for isolated CBE. We employed discovery and follow-up samples comprising 218 cases/865 controls and 78 trios in total, all of European descent. Our discovery sample identified a marker near SALL1, showing genome-wide significant association with CBE. However, analyses performed on follow-up samples did not add further support to these findings. We were also able to identify an association with CBE across our study samples (discovery: P = 8.88 × 10(-5); follow-up: P = 0.0025; combined: 1.09 × 10(-6)) in a highly conserved 32 kb intergenic region containing regulatory elements between WNT3 and WNT9B. Subsequent analyses in mice revealed expression for both genes in the genital region during stages relevant to the development of CBE in humans. Unfortunately, we were not able to replicate the suggestive signal for WNT3 and WNT9B in a sample that was enriched for non-CBE BEEC cases (P = 0.51). Our suggestive findings support the hypothesis that larger samples are warranted to identify association of common variation with CBE.
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Affiliation(s)
- Heiko Reutter
- Institute of Human Genetics Department of Neonatology, University of Bonn, Bonn, Germany
| | - Markus Draaken
- Institute of Human Genetics Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Tracie Pennimpede
- Developmental Genetics Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Developmental Genetics Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix F Brockschmidt
- Institute of Human Genetics Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Anne-Karolin Ebert
- Department of Urology and Pediatric Urology, University of Ulm, Ulm, Germany
| | | | - Wolfgang Rösch
- Department of Pediatric Urology, St. Hedwig Hospital Barmherzige Brüder, Regensburg, Germany
| | - Thomas M Boemers
- Department of Pediatric Surgery and Pediatric Urology, Children's Hospital of Cologne, Cologne, Germany
| | - Karin Hirsch
- Division of Paediatric Urology, Clinic of Urology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Eberhard Schmiedeke
- Department of Pediatric Surgery and Urology, Center for Child and Adolescent Health, Hospital Bremen-Mitte, Bremen, Germany
| | - Christian Meesters
- Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Tim Becker
- Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Raimund Stein
- Division of Pediatric Urology, University of Mainz, Mainz, Germany
| | - Boris Utsch
- Department of General Pediatrics and Neonatology, Center for Pediatric and Adolescent Care, Justus Liebig University, Gießen, Germany
| | | | - Agneta Nordenskjöld
- Woman and Child Health, Karolinska Institutet, Stockholm, Sweden Department of Pediatric Surgery, Astrid Lindgren Children Hospital, Stockholm, Sweden
| | - Gillian Barker
- Department of Women's and Children's Health, Pediatric Surgery, Uppsala University, Sweden
| | | | - Nadine Zwink
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Gundula Holmdahl
- Department of Pediatric Surgery, Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Göran Läckgren
- Section of Urology, Uppsala Academic Children Hospital, Uppsala, Sweden
| | - Ekkehart Jenetzky
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany Department of Child and Adolescent Psychiatry and Psychotherapy, Johannes-Gutenberg University, Mainz, Germany
| | - Wouter F J Feitz
- Department of Urology, Pediatric Urology Center, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | | | - Charlotte H W Wijers
- Department for Health Evidence, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Iris A L M Van Rooij
- Department for Health Evidence, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - John P Gearhart
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Bernhard G Herrmann
- Developmental Genetics Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Simeon A Boyadjiev
- Section of Genetics, Department of Pediatrics, University of California Davis, Sacramento, USA
| | - Markus M Nöthen
- Institute of Human Genetics Department of Neonatology, University of Bonn, Bonn, Germany
| | - Manuel Mattheisen
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA Department of Genomic Mathematics, University of Bonn, Bonn, Germany Department of Biomedicine, Aarhus University, Aarhus, Denmark
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24
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Werber M, Wittler L, Timmermann B, Grote P, Herrmann BG. The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo. Development 2014; 141:2325-30. [PMID: 24803591 DOI: 10.1242/dev.105858] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Differential gene expression is a prerequisite for the formation of multiple cell types from the fertilized egg during embryogenesis. Understanding the gene regulatory networks controlling cellular differentiation requires the identification of crucial differentially expressed control genes and, ideally, the determination of the complete transcriptomes of each individual cell type. Here, we have analyzed the transcriptomes of six major tissues dissected from mid-gestational (TS12) mouse embryos. Approximately one billion reads derived by RNA-seq analysis provided extended transcript lengths, novel first exons and alternative transcripts of known genes. We have identified 1375 genes showing tissue-specific expression, providing gene signatures for each of the six tissues. In addition, we have identified 1403 novel putative long noncoding RNA gene loci, 439 of which show differential expression. Our analysis provides the first complete transcriptome data for the mouse embryo. It offers a rich data source for the analysis of individual genes and gene regulatory networks controlling mid-gestational development.
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Affiliation(s)
- Martin Werber
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany Institute for Medical Genetics, Charité - University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
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25
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Draaken M, Baudisch F, Timmermann B, Kuhl H, Kerick M, Proske J, Wittler L, Pennimpede T, Ebert AK, Rösch W, Stein R, Bartels E, von Lowtzow C, Boemers TM, Herms S, Gearhart JP, Lakshmanan Y, Kockum CC, Holmdahl G, Läckgren G, Nordenskjöld A, Boyadjiev SA, Herrmann BG, Nöthen MM, Ludwig M, Reutter H. Classic bladder exstrophy: Frequent 22q11.21 duplications and definition of a 414 kb phenocritical region. ACTA ACUST UNITED AC 2014; 100:512-7. [DOI: 10.1002/bdra.23249] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Markus Draaken
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Friederike Baudisch
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Clinical Chemistry and Clinical Pharmacology; University of Bonn; Bonn Germany
| | - Bernd Timmermann
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Heiner Kuhl
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Martin Kerick
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Judith Proske
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Lars Wittler
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | | | - Wolfgang Rösch
- Department of Pediatric Urology; St. Hedwig Hospital Barmherzige Brμder; Regensburg Germany
| | - Raimund Stein
- Department of Urology; University of Mainz; Mainz Germany
| | - Enrika Bartels
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Catharina von Lowtzow
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Thomas M. Boemers
- Department of Pediatric Surgery and Pediatric Urology; Children's Hospital Cologne; Cologne Germany
| | - Stefan Herms
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
- Division of Medical Genetics and Department of Biomedicine; University of Basel; Basel Switzerland
| | - John P. Gearhart
- Division of Urology; The James Buchanan Brady Urological Institute; Johns Hopkins University School of Medicine; Baltimore
| | - Yegappan Lakshmanan
- Children's Hospital of Michigan; Department of Pediatric Urology; Detroit Michigan
| | | | - Gundela Holmdahl
- Department of Pediatric Surgery; Queen Silvia Children's Hospital; Gothenburg Sweden
| | - Göran Läckgren
- Section of Urology; Uppsala Academic Children Hospital; Uppsala Sweden
| | - Agnetha Nordenskjöld
- Department of Women's and Children's Health; Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
- Department of Pediatric Surgery; Astrid Lindgren Children's Hospital; Karolinska University Hospital; Stockholm Sweden
| | - Simeon A. Boyadjiev
- Section of Genetics; Department of Pediatrics; University of California Davis; Sacramento California
| | - Bernhard G. Herrmann
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Markus M. Nöthen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology; University of Bonn; Bonn Germany
| | - Heiko Reutter
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Neonatology; Children's Hospital; University of Bonn; Bonn Germany
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26
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Grote P, Herrmann BG. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol 2013; 10:1579-85. [PMID: 24036695 DOI: 10.4161/rna.26165] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetic control mechanisms determine active and silenced regions of the genome. It is known that the Polycomb Repressive Complex 2 (PRC2) and the Trithorax group/Mixed lineage leukemia (TrxG/Mll) complex are able to set repressive and active histone marks, respectively. Long non-coding RNAs (lncRNAs) can interact with either of these complexes and guide them to regulatory elements, thereby modifying the expression levels of target genes. The lncRNA Fendrr is transiently expressed in lateral mesoderm of mid-gestational mouse embryos and was shown to interact with both PRC2 and TrxG/Mll complexes in vivo. Gene targeting revealed that loss of Fendrr results in impaired differentiation of tissues derived from lateral mesoderm, the heart and the body wall, ultimately leading to embryonic death. Molecular data suggests that Fendrr acts via dsDNA/RNA triplex formation at target regulatory elements, and directly increases PRC2 occupancy at these sites. This, in turn, modifies the ratio of repressive to active marks, adjusting the expression levels of Fendrr target genes in lateral mesoderm. We propose that Fendrr also mediates long-term epigenetic marks to define expression levels of its target genes within the descendants of lateral mesoderm cells. Here we discuss approaches for lncRNA gene knockouts in the mouse, and suggest a model how Fendrr and possibly other lncRNAs act during embryogenesis.
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Affiliation(s)
- Phillip Grote
- Max Planck Institute for Molecular Genetics; Department Developmental Genetics; Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics; Department Developmental Genetics; Berlin, Germany
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27
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Hilger A, Schramm C, Pennimpede T, Wittler L, Dworschak GC, Bartels E, Engels H, Zink AM, Degenhardt F, Müller AM, Schmiedeke E, Grasshoff-Derr S, Märzheuser S, Hosie S, Holland-Cunz S, Wijers CHW, Marcelis CLM, van Rooij IALM, Hildebrandt F, Herrmann BG, Nöthen MM, Ludwig M, Reutter H, Draaken M. De novo microduplications at 1q41, 2q37.3, and 8q24.3 in patients with VATER/VACTERL association. Eur J Hum Genet 2013; 21:1377-82. [PMID: 23549274 DOI: 10.1038/ejhg.2013.58] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 11/09/2022] Open
Abstract
The acronym VATER/VACTERL association describes the combination of at least three of the following congenital anomalies: vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), renal malformations (R), and limb defects (L). We aimed to identify highly penetrant de novo copy number variations (CNVs) that contribute to VATER/VACTERL association. Array-based molecular karyotyping was performed in a cohort of 41 patients with VATER/VACTERL association and 6 patients with VATER/VACTERL-like phenotype including all of the patients' parents. Three de novo CNVs were identified involving chromosomal regions 1q41, 2q37.3, and 8q24.3 comprising one (SPATA17), two (CAPN10, GPR35), and three (EPPK1, PLEC, PARP10) genes, respectively. Pre-existing data from the literature prompted us to choose GPR35 and EPPK1 for mouse expression studies. Based on these studies, we prioritized GPR35 for sequencing analysis in an extended cohort of 192 patients with VATER/VACTERL association and VATER/VACTERL-like phenotype. Although no disease-causing mutation was identified, our mouse expression studies suggest GPR35 to be involved in the development of the VATER/VACTERL phenotype. Follow-up of GPR35 and the other genes comprising the identified duplications is warranted.
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Affiliation(s)
- Alina Hilger
- 1] Institute of Human Genetics, University of Bonn, Bonn, Germany [2] Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany [3] Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
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Grimm C, Chavez L, Vilardell M, Farrall AL, Tierling S, Böhm JW, Grote P, Lienhard M, Dietrich J, Timmermann B, Walter J, Schweiger MR, Lehrach H, Herwig R, Herrmann BG, Morkel M. DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet 2013; 9:e1003250. [PMID: 23408899 PMCID: PMC3567140 DOI: 10.1371/journal.pgen.1003250] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 06/21/2012] [Accepted: 12/02/2012] [Indexed: 12/31/2022] Open
Abstract
Aberrant CpG methylation is a universal epigenetic trait of cancer cell genomes. However, human cancer samples or cell lines preclude the investigation of epigenetic changes occurring early during tumour development. Here, we have used MeDIP-seq to analyse the DNA methylome of APCMin adenoma as a model for intestinal cancer initiation, and we present a list of more than 13,000 recurring differentially methylated regions (DMRs) characterizing intestinal adenoma of the mouse. We show that Polycomb Repressive Complex (PRC) targets are strongly enriched among hypermethylated DMRs, and several PRC2 components and DNA methyltransferases were up-regulated in adenoma. We further demonstrate by bisulfite pyrosequencing of purified cell populations that the DMR signature arises de novo in adenoma cells rather than by expansion of a pre-existing pattern in intestinal stem cells or undifferentiated crypt cells. We found that epigenetic silencing of tumour suppressors, which occurs frequently in colon cancer, was rare in adenoma. Quite strikingly, we identified a core set of DMRs, which is conserved between mouse adenoma and human colon cancer, thus possibly revealing a global panel of epigenetically modified genes for intestinal tumours. Our data allow a distinction between early conserved epigenetic alterations occurring in intestinal adenoma and late stochastic events promoting colon cancer progression, and may facilitate the selection of more specific clinical epigenetic biomarkers. The formation and progression of tumours to metastatic disease is driven by two major mechanisms, i.e. genetic alterations that activate oncogenes or inactivate tumour suppressor genes, and changes in the epigenome that cause variations in the expression of the genetic information. A deeper understanding of the interaction between the genetic and epigenetic mechanisms is critical for the selection of tumour biomarkers and for the future development of therapies. Human tumour specimens and cell lines contain a plethora of genetic and epigenetic changes, which complicate data analysis. In contrast, mouse tumour models such as the APCMin mouse used in this study arise by a single initiating genetic mutation, yet share key traits with human cancer. Here we show that mouse adenomas acquire a multitude of epigenetic alterations, which are recurring in mouse adenoma and in human colon cancer, representing early and advanced tumours, respectively. The use of a mouse model thus allowed us to uncover a sequence of epigenetic changes occurring in tumours, which may facilitate the identification of novel clinical colon cancer biomarkers.
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Affiliation(s)
- Christina Grimm
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Department of Rheumatology, Berlin, Germany
| | - Lukas Chavez
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Mireia Vilardell
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Alexandra L. Farrall
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Sascha Tierling
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Julia W. Böhm
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Phillip Grote
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Matthias Lienhard
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Jörn Dietrich
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Next Generation Sequencing Core Facility, Berlin, Germany
| | - Jörn Walter
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Michal R. Schweiger
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernhard G. Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Laboratory of Molecular Tumor Pathology, Berlin, Germany
- * E-mail:
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Draaken M, Mughal SS, Pennimpede T, Wolter S, Wittler L, Ebert AK, Rösch W, Stein R, Bartels E, Schmidt D, Boemers TM, Schmiedeke E, Hoffmann P, Moebus S, Herrmann BG, Nöthen MM, Reutter H, Ludwig M. Isolated bladder exstrophy associated with a de novo 0.9 Mb microduplication on chromosome 19p13.12. ACTA ACUST UNITED AC 2013; 97:133-9. [PMID: 23359465 DOI: 10.1002/bdra.23112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/12/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND The exstrophy-epispadias complex (BEEC) is a urogenital birth defect of varying severity. The causes of the BEEC are likely to be heterogeneous, with individual environmental or genetic risk factors still being largely unknown. In this study, we aimed to identify de novo causative copy number variations (CNVs) that contribute to the BEEC. METHODS Array-based molecular karyotyping was performed to screen 110 individuals with BEEC. Promising CNVs were tested for de novo occurrence by investigating parental DNAs. Genes located in regions of rearrangements were prioritized through expression analysis in mice to be sequenced in the complete cohort, to identify high-penetrance mutations involving small sequence changes. RESULTS A de novo 0.9 Mb microduplication involving chromosomal region 19p13.12 was identified in a single patient. This region harbors 20 validated RefSeq genes, and in situ hybridization data showed specific expression of the Wiz gene in regions surrounding the cloaca and the rectum between GD 9.5 and 13.5. Sanger sequencing of the complete cohort did not reveal any pathogenic alterations affecting the coding region of WIZ. CONCLUSIONS The present study suggests chromosomal region 19p13.12 as possibly involved in the development of CBE, but further studies are needed to prove a causal relation. The spatiotemporal expression patterns determined for the genes encompassed suggest a role for Wiz in the development of the phenotype. Our mutation screening, however, could not confirm that WIZ mutations are a frequent cause of CBE, although rare mutations might be detectable in larger patient samples. 19p13.12, microduplication, bladder exstrophy-epispadias complex, array-based molecular karyotyping, in situ hybridization analysis, copy number variations, WIZ gene.
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Affiliation(s)
- Markus Draaken
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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30
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Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, Herrmann BG. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 2013; 24:206-14. [PMID: 23369715 PMCID: PMC4149175 DOI: 10.1016/j.devcel.2012.12.012] [Citation(s) in RCA: 737] [Impact Index Per Article: 67.0] [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: 04/24/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/22/2022]
Abstract
The histone-modifying complexes PRC2 and TrxG/MLL play pivotal roles in determining the activation state of genes controlling pluripotency, lineage commitment, and cell differentiation. Long noncoding RNAs (lncRNAs) can bind to either complex, and some have been shown to act as modulators of PRC2 or TrxG/MLL activity. Here we show that the lateral mesoderm-specific lncRNA Fendrr is essential for proper heart and body wall development in the mouse. Embryos lacking Fendrr displayed upregulation of several transcription factors controlling lateral plate or cardiac mesoderm differentiation, accompanied by a drastic reduction in PRC2 occupancy along with decreased H3K27 trimethylation and/or an increase in H3K4 trimethylation at their promoters. Fendrr binds to both the PRC2 and TrxG/MLL complexes, suggesting that it acts as modulator of chromatin signatures that define gene activity. Thus, we identified an lncRNA that plays an essential role in the regulatory networks controlling the fate of lateral mesoderm derivatives.
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Affiliation(s)
- Phillip Grote
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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31
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Pennimpede T, Proske J, König A, Vidigal JA, Morkel M, Bramsen JB, Herrmann BG, Wittler L. In vivo knockdown of Brachyury results in skeletal defects and urorectal malformations resembling caudal regression syndrome. Dev Biol 2012; 372:55-67. [PMID: 22995555 DOI: 10.1016/j.ydbio.2012.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 08/20/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
The T-box transcription factor BRACHYURY (T) is a key regulator of mesoderm formation during early development. Complete loss of T has been shown to lead to embryonic lethality around E10.0. Here we characterize an inducible miRNA-based in vivo knockdown mouse model of T, termed KD3-T, which exhibits a hypomorphic phenotype. KD3-T embryos display axial skeletal defects caused by apoptosis of paraxial mesoderm, which is accompanied by urorectal malformations resembling the murine uro-recto-caudal syndrome and human caudal regression syndrome phenotypes. We show that there is a reduction of T in the notochord of KD3-T embryos which results in impaired notochord differentiation and its subsequent loss, whereas levels of T in the tailbud are sufficient for axis extension and patterning. Furthermore, the notochord in KD3-T embryos adopts a neural character and loses its ability to act as a signaling center. Since KD3-T animals survive until birth, they are useful for examining later roles for T in the development of urorectal tissues.
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Affiliation(s)
- Tracie Pennimpede
- Max Planck Institute for Molecular Genetics, Developmental Genetics Department, Ihnestraße 73, 14195 Berlin, Germany
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32
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Farrall AL, Riemer P, Leushacke M, Sreekumar A, Grimm C, Herrmann BG, Morkel M. Wnt and BMP signals control intestinal adenoma cell fates. Int J Cancer 2012; 131:2242-52. [PMID: 22344573 DOI: 10.1002/ijc.27500] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 02/07/2012] [Indexed: 12/20/2022]
Abstract
Cellular hierarchies and signals that govern stemness and differentiation of intestinal adenoma cells are not well defined. In this study, we used organotypic culture to investigate the impact of β-catenin and BMP signals in cells that form intestinal adenoma in the mouse. We found that activation of β-catenin signaling by loss of APC or transgenic induction of oncogenic mutant β-catenin (Ctnnb1(mut) ) initiates the conversion of untransformed intestinal cells to tumor cells. These tumor cells display cancer stem cell (CSC) traits such as increased expression of the CSC markers Cd133 and Cd44, a high capacity for self-renewal and unlimited proliferative potential. Subsequent inactivation of transgenic Ctnnb1(mut) results in the reversion of tumor cells to normal intestinal stem cells, which immediately reinstall the cellular hierarchy of the normal intestinal epithelium. Our data demonstrate that oncogenic activation of β-catenin signaling initiates the early steps of intestinal cellular transformation in the absence of irreversible genetic or epigenetic changes. Interestingly, we found that tumor cells in culture and in adenoma produce BMP4, which counteracts CSC-like traits by initiating irreversible cellular differentiation and loss of self-renewal capacity. We conclude that the opposition of stemness-maintaining oncogenic β-catenin signals and autocrine differentiating BMP signals within the adenoma cell provides a rationale for the formation of cellular hierarchies in intestinal adenoma and may serve to limit adenoma growth.
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Affiliation(s)
- Alexandra L Farrall
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
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33
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Bauer H, Schindler S, Charron Y, Willert J, Kusecek B, Herrmann BG. The nucleoside diphosphate kinase gene Nme3 acts as quantitative trait locus promoting non-Mendelian inheritance. PLoS Genet 2012; 8:e1002567. [PMID: 22438820 PMCID: PMC3305403 DOI: 10.1371/journal.pgen.1002567] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [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: 08/17/2011] [Accepted: 01/16/2012] [Indexed: 11/18/2022] Open
Abstract
The t-haplotype, a variant form of the t-complex region on mouse chromosome 17, acts as selfish genetic element and is transmitted at high frequencies (> 95%) from heterozygous (t/+) males to their offspring. This phenotype is termed transmission ratio distortion (TRD) and is caused by the interaction of the t-complex responder (Tcr) with several quantitative trait loci (QTL), the t-complex distorters (Tcd1 to Tcd4), all located within the t-haplotype region. Current data suggest that the distorters collectively impair motility of all sperm derived from t/+ males; t-sperm is rescued by the responder, whereas (+)-sperm remains partially dysfunctional. Recently we have identified two distorters as regulators of RHO small G proteins. Here we show that the nucleoside diphosphate kinase gene Nme3 acts as a QTL on TRD. Reduction of the Nme3 dosage by gene targeting of the wild-type allele enhanced the transmission rate of the t-haplotype and phenocopied distorter function. Genetic and biochemical analysis showed that the t-allele of Nme3 harbors a mutation (P89S) that compromises enzymatic activity of the protein and genetically acts as a hypomorph. Transgenic overexpression of the Nme3 t-allele reduced t-haplotype transmission, proving it to be a distorter. We propose that the NME3 protein interacts with RHO signaling cascades to impair sperm motility through hyperactivation of SMOK, the wild-type form of the responder. This deleterious effect of the distorters is counter-balanced by the responder, SMOK(Tcr), a dominant-negative protein kinase exclusively expressed in t-sperm, thus permitting selfish behaviour and preferential transmission of the t-haplotype. In addition, the previously reported association of NME family members with RHO signaling in somatic cell motility and metastasis, in conjunction with our data involving RHO signaling in sperm motility, suggests a functional conservation between mechanisms for motility control in somatic cells and spermatozoa.
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Affiliation(s)
- Hermann Bauer
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Leushacke M, Spörle R, Bernemann C, Brouwer-Lehmitz A, Fritzmann J, Theis M, Buchholz F, Herrmann BG, Morkel M. An RNA interference phenotypic screen identifies a role for FGF signals in colon cancer progression. PLoS One 2011; 6:e23381. [PMID: 21853123 PMCID: PMC3154943 DOI: 10.1371/journal.pone.0023381] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [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: 02/25/2011] [Accepted: 07/15/2011] [Indexed: 12/19/2022] Open
Abstract
In tumor cells, stepwise oncogenic deregulation of signaling cascades induces alterations of cellular morphology and promotes the acquisition of malignant traits. Here, we identified a set of 21 genes, including FGF9, as determinants of tumor cell morphology by an RNA interference phenotypic screen in SW480 colon cancer cells. Using a panel of small molecular inhibitors, we subsequently established phenotypic effects, downstream signaling cascades, and associated gene expression signatures of FGF receptor signals. We found that inhibition of FGF signals induces epithelial cell adhesion and loss of motility in colon cancer cells. These effects are mediated via the mitogen-activated protein kinase (MAPK) and Rho GTPase cascades. In agreement with these findings, inhibition of the MEK1/2 or JNK cascades, but not of the PI3K-AKT signaling axis also induced epithelial cell morphology. Finally, we found that expression of FGF9 was strong in a subset of advanced colon cancers, and overexpression negatively correlated with patients' survival. Our functional and expression analyses suggest that FGF receptor signals can contribute to colon cancer progression.
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Affiliation(s)
- Marc Leushacke
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, Germany
| | - Ralf Spörle
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christof Bernemann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Antje Brouwer-Lehmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johannes Fritzmann
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Mirko Theis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- University Hospital Carl Gustav Carus and Medical Faculty, University of Technology Dresden, Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- University Hospital Carl Gustav Carus and Medical Faculty, University of Technology Dresden, Dresden, Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Markus Morkel
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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Timmermann B, Kerick M, Roehr C, Fischer A, Isau M, Boerno ST, Wunderlich A, Barmeyer C, Seemann P, Koenig J, Lappe M, Kuss AW, Garshasbi M, Bertram L, Trappe K, Werber M, Herrmann BG, Zatloukal K, Lehrach H, Schweiger MR. Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis. PLoS One 2010; 5:e15661. [PMID: 21203531 PMCID: PMC3008745 DOI: 10.1371/journal.pone.0015661] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [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: 08/25/2010] [Accepted: 11/19/2010] [Indexed: 01/11/2023] Open
Abstract
Background Colorectal cancer (CRC) is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. Methodology/Principal Findings Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS) and microsatellite instable (MSI) colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. Conclusions/Significance We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations.
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Affiliation(s)
- Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christina Roehr
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University, Berlin, Germany
| | - Axel Fischer
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melanie Isau
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University, Berlin, Germany
| | - Stefan T. Boerno
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University, Berlin, Germany
| | - Andrea Wunderlich
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University, Berlin, Germany
| | - Christian Barmeyer
- Department of Gastroenterology, Charité Universitätsmedizin, Berlin, Germany
| | - Petra Seemann
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin, Berlin, Germany
| | - Jana Koenig
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin, Berlin, Germany
| | - Michael Lappe
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas W. Kuss
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Human Genetics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Masoud Garshasbi
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Bertram
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kathrin Trappe
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Werber
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kurt Zatloukal
- Department of Pathology, Medical University, Graz, Austria
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R. Schweiger
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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Vidigal JA, Morkel M, Wittler L, Brouwer-Lehmitz A, Grote P, Macura K, Herrmann BG. An inducible RNA interference system for the functional dissection of mouse embryogenesis. Nucleic Acids Res 2010; 38:e122. [PMID: 20350929 PMCID: PMC2887975 DOI: 10.1093/nar/gkq199] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [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: 11/13/2022] Open
Abstract
Functional analysis of multiple genes is key to understanding gene regulatory networks controlling embryonic development. We have developed an integrated vector system for inducible gene silencing by shRNAmir-mediated RNA interference in mouse embryos, as a fast method for dissecting mammalian gene function. For validation of the vector system, we generated mutant phenotypes for Brachyury, Foxa2 and Noto, transcription factors which play pivotal roles in embryonic development. Using a series of Brachyury shRNAmir vectors of various strengths we generated hypomorphic and loss of function phenotypes allowing the identification of Brachyury target genes involved in trunk development. We also demonstrate temporal control of gene silencing, thus bypassing early embryonic lethality. Importantly, off-target effects of shRNAmir expression were not detectable. Taken together, the system allows the dissection of gene function at unprecedented detail and speed, and provides tight control of the genetic background minimizing intrinsic variation.
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Affiliation(s)
- Joana A Vidigal
- Max-Planck-Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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Véron N, Bauer H, Weisse AY, Lüder G, Werber M, Herrmann BG. Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder. Genes Dev 2009; 23:2705-10. [PMID: 19952105 DOI: 10.1101/gad.553009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The t complex responder (Tcr) encoded by the mouse t haplotype is able to cause phenotypic differences between t and + sperm derived from t/+ males, leading to non-Mendelian inheritance. This capability of Tcr contradicts the concept of phenotypic equivalence proposed for sperm cells, which develop in a syncytium and actively share gene products. By analyzing a Tcr minigene in hemizygous transgenic mice, we show that Tcr gene products are post-meiotically expressed and are retained in the haploid sperm cells. The wild-type allele of Tcr, sperm motility kinase-1 (Smok1), behaves in the same manner, suggesting that Tcr/Smok reveal a common mechanism prone to evolve non-Mendelian inheritance in mammals.
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Affiliation(s)
- Nathalie Véron
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, 14195 Berlin, Germany
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38
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Abstract
The murine developmental mutation T identifies a gene required in mesoderm formation. T/T mutant embryos develop normally to the primitive streak stage; during early organogenesis they show insufficient mesoderm and absence of the notochord. The mutants die at around 10 days of gestation because of the lack of the allantois. We have localized the T mutation relative to DNA markers and used a combination of genetic and molecular techniques to clone the T gene. Expression of the T gene is restricted to nascent mesoderm and to the notochord, the tissues most strongly affected by the mutation. Recent results suggest that the T gene encodes a nuclear factor involved in establishing notochord cell identity and differentiation, and is directly or indirectly involved in the organization of axial development.
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Affiliation(s)
- B G Herrmann
- Max-Planck-Institut für Entwicklungsbiologie, Abteilung Biochemie, Tübingen, Germany
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39
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Wittler L, Shin EH, Grote P, Kispert A, Beckers A, Gossler A, Werber M, Herrmann BG. Expression of Msgn1 in the presomitic mesoderm is controlled by synergism of WNT signalling and Tbx6. EMBO Rep 2007; 8:784-9. [PMID: 17668009 PMCID: PMC1978083 DOI: 10.1038/sj.embor.7401030] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [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: 12/20/2006] [Revised: 06/04/2007] [Accepted: 06/05/2007] [Indexed: 11/09/2022] Open
Abstract
The vertebral column and skeletal muscles of vertebrates are derived from the paraxial mesoderm, which is laid down initially as two stripes of mesenchymal cells alongside the neural tube and subsequently segmented. Previous work has shown that the wingless-type MMTV integration site family (WNT), fibroblast growth factor- and Delta-Notch signalling pathways control presomitic mesoderm (psm) formation and segmentation. Here, we show that the expression of mesogenin 1, a basic helix-loop-helix transcription factor, which is essential for psm maturation, is regulated by synergism between WNT signalling and the T-box 6 transcription factor, involving a feed-forward control mechanism. These findings emphasize the crucial role of WNT signalling in the control of psm formation, maturation and segmentation.
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Affiliation(s)
- Lars Wittler
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
- Institute of Medical Genetics, Charité-University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, Berlin 12200, Germany
| | - Eun-ha Shin
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
- Institute of Medical Genetics, Charité-University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, Berlin 12200, Germany
| | - Andreas Kispert
- Institute for Molecular Biology OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover D-30625, Germany
| | - Anja Beckers
- Institute for Molecular Biology OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover D-30625, Germany
| | - Achim Gossler
- Institute for Molecular Biology OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover D-30625, Germany
| | - Martin Werber
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
- Institute of Medical Genetics, Charité-University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, Berlin 12200, Germany
- Tel: +49 30 8413 1344; Fax: +49 30 8413 1229; E-mail:
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40
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Kolanczyk M, Kossler N, Kühnisch J, Lavitas L, Stricker S, Wilkening U, Manjubala I, Fratzl P, Spörle R, Herrmann BG, Parada LF, Kornak U, Mundlos S. Multiple roles for neurofibromin in skeletal development and growth. Hum Mol Genet 2007; 16:874-86. [PMID: 17317783 DOI: 10.1093/hmg/ddm032] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a prevalent genetic disorder primarily characterized by the formation of neurofibromas, café-au-lait spots and freckling. Skeletal abnormalities such as short stature or bowing/pseudarthrosis of the tibia are relatively common. To investigate the role of the neurofibromin in skeletal development, we crossed Nf1flox mice with Prx1Cre mice to inactivate Nf1 in undifferentiated mesenchymal cells of the developing limbs. Similar to NF1 affected individuals, Nf1(Prx1) mice show bowing of the tibia and diminished growth. Tibial bowing is caused by decreased stability of the cortical bone due to a high degree of porosity, decreased stiffness and reduction in the mineral content as well as hyperosteoidosis. Accordingly, osteoblasts show an increase in proliferation and a decreased ability to differentiate and mineralize in vitro. The reduction in growth is due to lower proliferation rates and a differentiation defect of chondrocytes. Abnormal vascularization of skeletal tissues is likely to contribute to this pathology as it exerts a negative effect on cortical bone stability. Furthermore, Nf1 has an important role in the development of joints, as shown by fusion of the hip joints and other joint abnormalities, which are not observed in neurofibromatosis type I. Thus, neurofibromin has multiple essential roles in skeletal development and growth.
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Affiliation(s)
- Mateusz Kolanczyk
- FG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
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41
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Bauer H, Véron N, Willert J, Herrmann BG. The t-complex-encoded guanine nucleotide exchange factor Fgd2 reveals that two opposing signaling pathways promote transmission ratio distortion in the mouse. Genes Dev 2007; 21:143-7. [PMID: 17234881 PMCID: PMC1770897 DOI: 10.1101/gad.414807] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transmission ratio distortion (TRD), the preferential inheritance of the t haplotype from t/+ males, is caused by the cooperative effect of four t-complex distorters (Tcd1-4) and the single t-complex responder (Tcr) on sperm motility. Here we show that Fgd2, encoding a Rho guanine nucleotide exchange factor, maps to the Tcd2 region. The t allele of Fgd2 is overexpressed in testis compared with wild type. A loss-of-function allele of Fgd2 generated by gene targeting reduces the transmission ratio of the t haplotype t(h49), directly demonstrating the role of Fgd2 as Distorter. Fgd2 identifies a second Rho G protein signaling pathway promoting TRD.
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Affiliation(s)
- Hermann Bauer
- Max-Planck-Institute for Molecular Genetics, Department of Developmental Genetics, Berlin 14195, Germany.
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42
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Bauer H, Willert J, Koschorz B, Herrmann BG. The t complex–encoded GTPase-activating protein Tagap1 acts as a transmission ratio distorter in mice. Nat Genet 2005; 37:969-73. [PMID: 16116428 DOI: 10.1038/ng1617] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [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: 05/11/2005] [Accepted: 06/29/2005] [Indexed: 11/08/2022]
Abstract
Transmission ratio distortion in the mouse is caused by several t-complex distorters (Tcds) acting in trans on the t-complex responder (Tcr). Tcds additively affect the flagellar movement of all spermatozoa derived from t/+ males; sperm carrying Tcr are rescued, resulting in an advantage for t sperm in fertilization. Here we show that Tagap1, a GTPase-activating protein, can act as a distorter. Tagap1 maps to the Tcd1 interval and has four t loci, which encode altered proteins including a C-terminally truncated form. Overexpression of wild-type Tagap1 in sperm cells phenocopied Tcd function, whereas a loss-of-function Tagap1 allele reduced the transmission rate of the t6 haplotype. The combined data strongly suggest that the t loci of Tagap1 produce Tcd1a. Our results unravel the molecular nature of a Tcd and demonstrate the importance of small G proteins in transmission ratio distortion in the mouse.
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Affiliation(s)
- Hermann Bauer
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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43
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Hofmann M, Schuster-Gossler K, Watabe-Rudolph M, Aulehla A, Herrmann BG, Gossler A. WNT signaling, in synergy with T/TBX6, controls Notch signaling by regulating Dll1 expression in the presomitic mesoderm of mouse embryos. Genes Dev 2004; 18:2712-7. [PMID: 15545628 PMCID: PMC528888 DOI: 10.1101/gad.1248604] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Notch signaling in the presomitic mesoderm (psm) is critical for somite formation and patterning. Here, we show that WNT signals regulate transcription of the Notch ligand Dll1 in the tailbud and psm. LEF/TCF factors cooperate with TBX6 to activate transcription from the Dll1 promoter in vitro. Mutating either T or LEF/TCF sites in the Dll1 promoter abolishes reporter gene expression in vitro as well as in the tail bud and psm of transgenic embryos. Our results indicate that WNT activity, in synergy with TBX6, regulates Dll1 transcription and thereby controls Notch activity, somite formation, and patterning.
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Affiliation(s)
- Michael Hofmann
- Max-Planck-Institute of Immunobiology, Stübeweg 51, D-79108 Freiburg, Germany
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44
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Abstract
The vertebral column is derived from somites formed by segmentation of presomitic mesoderm, a fundamental process of vertebrate embryogenesis. Models on the mechanism controlling this process date back some three to four decades. Access to understanding the molecular control of somitogenesis has been gained only recently by the discovery of molecular oscillators (segmentation clock) and gradients of signaling molecules, as predicted by early models. The Notch signaling pathway is linked to the oscillator and plays a decisive role in inter- and intrasomitic boundary formation. An Fgf8 signaling gradient is involved in somite size control. And the (canonical) Wnt signaling pathway, driven by Wnt3a, appears to integrate clock and gradient in a global mechanism controlling the segmentation process. In this review, we discuss recent advances in understanding the molecular mechanism controlling somitogenesis.
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Affiliation(s)
- Alexander Aulehla
- Max-Planck-Institute for Molecular Genetics, Department of Developmental Genetics, 14195 Berlin, Germany
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45
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Abdelkhalek HB, Beckers A, Schuster-Gossler K, Pavlova MN, Burkhardt H, Lickert H, Rossant J, Reinhardt R, Schalkwyk LC, Müller I, Herrmann BG, Ceolin M, Rivera-Pomar R, Gossler A. The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation. Genes Dev 2004; 18:1725-36. [PMID: 15231714 PMCID: PMC478193 DOI: 10.1101/gad.303504] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The floating head (flh) gene in zebrafish encodes a homeodomain protein, which is essential for notochord formation along the entire body axis. flh orthologs, termed Not genes, have been isolated from chick and Xenopus, but no mammalian ortholog has yet been identified. Truncate (tc) is an autosomal recessive mutation in mouse that specifically disrupts the development of the caudal notochord. Here, we demonstrate that truncate arose by a mutation in the mouse Not gene. The truncate allele (Nottc) contains a point mutation in the homeobox of Not that changes a conserved Phenylalanine residue in helix 1 to a Cysteine (F20C), and significantly destabilizes the homeodomain. Reversion of F20C in one allele of homozygous tc embryonic stem (ES) cells is sufficient to restore normal notochord formation in completely ES cell-derived embryos. We have generated a targeted mutation of Not by replacing most of the Not coding sequence, including the homeobox with the eGFP gene. The phenotype of NoteGFP/eGFP, NoteGFP/tc, and Nottc/tc embryos is very similar but slightly more severe in NoteGFP/eGFP than in Nottc/tc embryos. This confirms allelism of truncate and Not, and indicates that tc is not a complete null allele. Not expression is abolished in Foxa2 and T mutant embryos, suggesting that Not acts downstream of both genes during notochord development. This is in contrast to zebrafish embryos, in which flh interacts with ntl (zebrafish T) in a regulatory loop and is essential for development of the entire notochord, and suggests that different genetic control circuits act in different vertebrate species during notochord formation.
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Affiliation(s)
- Hanaa Ben Abdelkhalek
- Institute for Molecular Biology OE5250, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
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46
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Aulehla A, Wehrle C, Brand-Saberi B, Kemler R, Gossler A, Kanzler B, Herrmann BG. Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev Cell 2003; 4:395-406. [PMID: 12636920 DOI: 10.1016/s1534-5807(03)00055-8] [Citation(s) in RCA: 434] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The vertebral column derives from somites generated by segmentation of presomitic mesoderm (PSM). Somitogenesis involves a molecular oscillator, the segmentation clock, controlling periodic Notch signaling in the PSM. Here, we establish a novel link between Wnt/beta-catenin signaling and the segmentation clock. Axin2, a negative regulator of the Wnt pathway, is directly controlled by Wnt/beta-catenin and shows oscillating expression in the PSM, even when Notch signaling is impaired, alternating with Lfng expression. Moreover, Wnt3a is required for oscillating Notch signaling activity in the PSM. We propose that the segmentation clock is established by Wnt/beta-catenin signaling via a negative-feedback mechanism and that Wnt3a controls the segmentation process in vertebrates.
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Affiliation(s)
- Alexander Aulehla
- Abteilung Entwicklungsbiologie, Max-Planck-Institut für Immunbiologie, Stübeweg 51, D-79108, Freiburg, Germany
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47
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Gitton Y, Dahmane N, Baik S, Ruiz i Altaba A, Neidhardt L, Scholze M, Herrmann BG, Kahlem P, Benkahla A, Schrinner S, Yildirimman R, Herwig R, Lehrach H, Yaspo ML. A gene expression map of human chromosome 21 orthologues in the mouse. Nature 2002; 420:586-90. [PMID: 12466855 DOI: 10.1038/nature01270] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [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: 06/11/2002] [Accepted: 09/12/2002] [Indexed: 01/22/2023]
Abstract
The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular characterization of all of its genes. Trisomy 21 is associated with Down's syndrome, the most common genetic cause of mental retardation in humans. The phenotype includes various organ dysmorphies, stereotypic craniofacial anomalies and brain malformations. Molecular analysis of congenital aneuploidies poses a particular challenge because the aneuploid region contains many protein-coding genes whose function is unknown. One essential step towards understanding their function is to analyse mRNA expression patterns at key stages of organism development. Seminal works in flies, frogs and mice showed that genes whose expression is restricted spatially and/or temporally are often linked with specific ontogenic processes. Here we describe expression profiles of mouse orthologues to HSA21 genes by a combination of large-scale mRNA in situ hybridization at critical stages of embryonic and brain development and in silico (computed) mining of expressed sequence tags. This chromosome-scale expression annotation associates many of the genes tested with a potential biological role and suggests candidates for the pathogenesis of Down's syndrome.
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Affiliation(s)
- Yorick Gitton
- Skirball Institute, Developmental Genetics Program and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA
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48
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Klock A, Herrmann BG. Cloning and expression of the mouse dual-specificity mitogen-activated protein (MAP) kinase phosphatase Mkp3 during mouse embryogenesis. Mech Dev 2002; 116:243-7. [PMID: 12128234 DOI: 10.1016/s0925-4773(02)00153-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mitogen-activated protein (MAP) kinase phosphatases (MKPs) constitute a growing family of dual specificity phosphatases, which dephosphorylate both serine/threonine and tyrosine residues of MAP kinases. MAP kinase signaling cascades are involved in the control of cell proliferation, differentiation and apoptosis. In mammals, ten members of the dual-specificity MKP family have so far been identified. In this report, we describe the cloning and expression analysis of the mouse Mkp3 gene. During early development, expression of Mkp3 is most prominent in the primitive streak, presomitic mesoderm and somites, frontonasal prominence, midbrain/hindbrain boundary, branchial arches and limb buds. At later stages, expression is also detected in the tooth primordia, vibrissae, hair follicles, pinna, submandibular gland, mammary gland primordia, lung and kidney. Strong expression was detected in the adult brain.
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Affiliation(s)
- Andrea Klock
- Max-Planck-Institut für Immunbiologie, Abt. Entwicklungsbiologie, Stübeweg 51, 79108 Freiburg, Germany
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49
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Bernier G, Vukovich W, Neidhardt L, Herrmann BG, Gruss P. Isolation and characterization of a downstream target of Pax6 in the mammalian retinal primordium. Development 2001; 128:3987-94. [PMID: 11641222 DOI: 10.1242/dev.128.20.3987] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The transcription factor Pax6 is required for eye morphogenesis in humans, mice and insects, and can induce ectopic eye formation in vertebrate and invertebrate organisms. Although the role of Pax6 has intensively been studied, only a limited number of genes have been identified that depend on Pax6 activity for their expression in the mammalian visual system. Using a large-scale in situ hybridization screen approach, we have identified a novel gene expressed in the mouse optic vesicle. This gene, Necab, encodes a putative cytoplasmic Ca2+-binding protein and coincides with Pax6 expression pattern in the neural ectoderm of the optic vesicle and in the forebrain pretectum. Remarkably, Necab expression is absent in both structures in Pax6 mutant embryos. By contrast, the optic vesicle-expressed homeobox genes Rx, Six3, Otx2 and Lhx2 do not exhibit an altered expression pattern. Using gain-of-function experiments, we show that Pax6 can induce ectopic expression of Necab, suggesting that Necab is a direct or indirect transcriptional target of Pax6. In addition, we have found that Necab misexpression can induce ectopic expression of the homeobox gene Chx10, a transcription factor implicated in retina development. Taken together, our results provide evidence that Necab is genetically downstream of Pax6 and that it is a part of a signal transduction pathway in retina development.
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Affiliation(s)
- G Bernier
- Max Planck Institute of Biophysical Chemistry, Department of Molecular Cell Biology, Am Fassberg 11, 37077 Göttingen, Germany
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50
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Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, Lehrach H, Herrmann BG. Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev 2000; 98:77-94. [PMID: 11044609 DOI: 10.1016/s0925-4773(00)00453-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have adapted the whole-mount in situ hybridization technique to perform high-throughput gene expression analysis in mouse embryos. A large-scale screen for genes showing specific expression patterns in the mid-gestation embryo was carried out, and a large number of genes controlling development were isolated. From 35760 clones of a 9.5 d.p.c. cDNA library, a total of 5348 cDNAs, enriched for rare transcripts, were selected and analyzed by whole-mount in situ hybridization. Four hundred and twenty-eight clones revealed specific expression patterns in the 9.5 d.p.c. embryo. Of 361 tag-sequenced clones, 198 (55%) represent 154 known mouse genes. Thirty-nine (25%) of the known genes are involved in transcriptional regulation and 33 (21%) in inter- or intracellular signaling. A large number of these genes have been shown to play an important role in embryogenesis. Furthermore, 24 (16%) of the known genes are implicated in human disorders and three others altered in classical mouse mutations. Similar proportions of regulators of embryonic development and candidates for human disorders or mouse mutations are expected among the 163 new mouse genes isolated. Thus, high-throughput gene expression analysis is suitable for isolating regulators of embryonic development on a large-scale, and in the long term, for determining the molecular anatomy of the mouse embryo. This knowledge will provide a basis for the systematic investigation of pattern formation, tissue differentiation and organogenesis in mammals.
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Affiliation(s)
- L Neidhardt
- Max-Planck-Institut für Immunbiologie, Abt. Entwicklungsbiologie, Stübeweg 51, 79108, Freiburg, Germany
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