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Reissig TM, Tzianopoulos I, Liffers ST, Rosery VK, Guyot M, Ting S, Wiesweg M, Kasper S, Meister P, Herold T, Schmidt HH, Schumacher B, Albers D, Markus P, Treckmann J, Schuler M, Schildhaus HU, Siveke JT. Smaller panel, similar results: genomic profiling and molecularly informed therapy in pancreatic cancer. ESMO Open 2023; 8:101539. [PMID: 37148593 DOI: 10.1016/j.esmoop.2023.101539] [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: 02/04/2023] [Revised: 03/12/2023] [Accepted: 03/24/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Pancreatic cancer has a dismal prognosis. One reason is resistance to cytotoxic drugs. Molecularly matched therapies might overcome this resistance but the best approach to identify those patients who may benefit is unknown. Therefore, we sought to evaluate a molecularly guided treatment approach. MATERIALS AND METHODS We retrospectively analyzed the clinical outcome and mutational status of patients with pancreatic cancer who received molecular profiling at the West German Cancer Center Essen from 2016 to 2021. We carried out a 47-gene DNA next-generation sequencing (NGS) panel. Furthermore, we assessed microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) status and, sequentially and only in case of KRAS wild-type, gene fusions via RNA-based NGS. Patient data and treatment were retrieved from the electronic medical records. RESULTS Of 190 included patients, 171 had pancreatic ductal adenocarcinoma (90%). One hundred and three patients had stage IV pancreatic cancer at diagnosis (54%). MMR analysis in 94 patients (94/190, 49.5%) identified 3 patients with dMMR (3/94, 3.2%). Notably, we identified 32 patients with KRAS wild-type status (16.8%). To identify driver alterations in these patients, we conducted an RNA-based fusion assay on 13 assessable samples and identified 5 potentially actionable fusions (5/13, 38.5%). Overall, we identified 34 patients with potentially actionable alterations (34/190, 17.9%). Of these 34 patients, 10 patients (10/34, 29.4%) finally received at least one molecularly targeted treatment and 4 patients had an exceptional response (>9 months on treatment). CONCLUSIONS Here, we show that a small-sized gene panel can suffice to identify relevant therapeutic options for pancreatic cancer patients. Informally comparing with previous large-scale studies, this approach yields a similar detection rate of actionable targets. We propose molecular sequencing of pancreatic cancer as standard of care to identify KRAS wild-type and rare molecular subsets for targeted treatment strategies.
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Affiliation(s)
- T M Reissig
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Heidelberg, Germany; Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - I Tzianopoulos
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Heidelberg, Germany; Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - S-T Liffers
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - V K Rosery
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Heidelberg, Germany; Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - M Guyot
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; Department of Gastroenterology, Oncology und Hematology, Diabetology and Rheumatology, Marien-Hospital Wesel, Wesel, Germany
| | - S Ting
- Institute of Pathology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - M Wiesweg
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - S Kasper
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - P Meister
- Department of General, Visceral and Transplantation Surgery, Hepatology, and Transplant Medicine, University Hospital Essen, Essen, Germany
| | - T Herold
- Institute of Pathology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - H H Schmidt
- Department of Gastroenterology, Hepatology, and Transplant Medicine, University Hospital Essen, Essen, Germany
| | - B Schumacher
- Department of Gastroenterology, Visceral and Trauma Surgery, Elisabeth Hospital Essen, Essen, Germany
| | - D Albers
- Department of Gastroenterology, Visceral and Trauma Surgery, Elisabeth Hospital Essen, Essen, Germany
| | - P Markus
- Department of General, Visceral and Trauma Surgery, Elisabeth Hospital Essen, Essen, Germany
| | - J Treckmann
- Department of General, Visceral and Transplantation Surgery, Hepatology, and Transplant Medicine, University Hospital Essen, Essen, Germany
| | - M Schuler
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - H-U Schildhaus
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany; Institute of Pathology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - J T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Heidelberg, Germany; Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany.
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Gitchev T, Zala G, Meister P, Jost D. 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. Bioinformatics 2022; 38:5454-5456. [PMID: 36355469 PMCID: PMC9750120 DOI: 10.1093/bioinformatics/btac705] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/05/2022] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Here, we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data. AVAILABILITY AND IMPLEMENTATION Software available at https://gitlab.com/togop/3DPolyS-LE; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux and Mac OS). SUPPLEMENTARY INFORMATION Supplementary information are available at Bioinformatics online.
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Affiliation(s)
| | - Gabriel Zala
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | | | - Daniel Jost
- To whom correspondence should be addressed. or
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Vazquez-Pianzola P, Beuchle D, Saro G, Hernández G, Maldonado G, Brunßen D, Meister P, Suter B. Female meiosis II and pronuclear fusion require the microtubule transport factor Bicaudal D. Development 2022; 149:275749. [DOI: 10.1242/dev.199944] [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: 07/01/2021] [Accepted: 05/25/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Bicaudal D (BicD) is a dynein adaptor that transports different cargoes along microtubules. Reducing the activity of BicD specifically in freshly laid Drosophila eggs by acute protein degradation revealed that BicD is needed to produce normal female meiosis II products, to prevent female meiotic products from re-entering the cell cycle, and for pronuclear fusion. Given that BicD is required to localize the spindle assembly checkpoint (SAC) components Mad2 and BubR1 to the female meiotic products, it appears that BicD functions to localize these components to control metaphase arrest of polar bodies. BicD interacts with Clathrin heavy chain (Chc), and both proteins localize to centrosomes, mitotic spindles and the tandem spindles during female meiosis II. Furthermore, BicD is required to localize clathrin and the microtubule-stabilizing factors transforming acidic coiled-coil protein (D-TACC/Tacc) and Mini spindles (Msps) correctly to the meiosis II spindles, suggesting that failure to localize these proteins may perturb SAC function. Furthermore, immediately after the establishment of the female pronucleus, D-TACC and Caenorhabditis elegans BicD, tacc and Chc are also needed for pronuclear fusion, suggesting that the underlying mechanism might be more widely used across species.
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Affiliation(s)
| | - Dirk Beuchle
- Institute of Cell Biology, University of Bern 1 , 3012 Berne , Switzerland
| | - Gabriella Saro
- Institute of Cell Biology, University of Bern 1 , 3012 Berne , Switzerland
| | - Greco Hernández
- Instituto Nacional de Cancerología (INCan) 2 Laboratory of Translation and Cancer, Unit of Biomedical Research on Cancer , , 14080-Tlalpan, Mexico City , Mexico
| | - Giovanna Maldonado
- Instituto Nacional de Cancerología (INCan) 2 Laboratory of Translation and Cancer, Unit of Biomedical Research on Cancer , , 14080-Tlalpan, Mexico City , Mexico
| | - Dominique Brunßen
- Institute of Cell Biology, University of Bern 1 , 3012 Berne , Switzerland
| | - Peter Meister
- Institute of Cell Biology, University of Bern 1 , 3012 Berne , Switzerland
| | - Beat Suter
- Institute of Cell Biology, University of Bern 1 , 3012 Berne , Switzerland
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Gómez-Saldivar G, Glauser DA, Meister P. Tissue-specific DamID protocol using nanopore sequencing. J Biol Methods 2021; 8:e152. [PMID: 34514013 PMCID: PMC8411031 DOI: 10.14440/jbm.2021.362] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
DNA adenine methylation identification (DamID) is a powerful method to determine DNA binding profiles of proteins at a genomic scale. The method leverages the fusion between a protein of interest and the Dam methyltransferase of E. coli, which methylates proximal DNA in vivo. Here, we present an optimized procedure, which was developed for tissue-specific analyses in Caenorhabditis elegans and successfully used to footprint genes actively transcribed by RNA polymerases and to map transcription factor binding in gene regulatory regions. The present protocol details C. elegans-specific steps involved in the preparation of transgenic lines and genomic DNA samples, as well as broadly applicable steps for the DamID procedure, including the isolation of methylated DNA fragments, the preparation of multiplexed libraries, Nanopore sequencing, and data analysis. Two distinctive features of the approach are (i) the use of an efficient recombination-based strategy to selectively analyze rare cell types and (ii) the use of Nanopore sequencing, which streamlines the process. The method allows researchers to go from genomic DNA samples to sequencing results in less than a week, while being sensitive enough to report reliable DNA footprints in cell types as rare as 2 cells per animal.
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Affiliation(s)
| | | | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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Osuna-Luque J, Ewald CY, Meister P. Widespread gpa-4 promoter-driven expression during Caenorhabditis elegans development. MicroPubl Biol 2021; 2021. [PMID: 34423282 PMCID: PMC8377519 DOI: 10.17912/micropub.biology.000443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/03/2022]
Abstract
The gpa-4 promoter-driven expression is described as specific for ASIL and ASIR chemosensory neurons in the nematode Caenorhabditis elegans, yet this was mostly examined in adult animals. Here we used a recombination-mediated reporter to test the previously used gpa-4 promoter expression. This reporter highlights all cells in which the gpa-4 promoter has been active at one point or another during development. We show that the gpa-4 promoter is indeed active in ASI, yet to our surprise, thispromoter drives also expression in many other cell types, including the somatic gonad, the seam cells, a subset of tail and head neurons, and muscle cells, demonstrating a widespread activity of this transgenic gpa-4 promoter during embryonic and post-embryonic development.
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Grosmaire M, Launay C, Siegwald M, Brugière T, Estrada-Virrueta L, Berger D, Burny C, Modolo L, Blaxter M, Meister P, Félix MA, Gouyon PH, Delattre M. Males as somatic investment in a parthenogenetic nematode. Science 2019; 363:1210-1213. [PMID: 30872523 DOI: 10.1126/science.aau0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
We report the reproductive strategy of the nematode Mesorhabditis belari This species produces only 9% males, whose sperm is necessary to fertilize and activate the eggs. However, most of the fertilized eggs develop without using the sperm DNA and produce female individuals. Only in 9% of eggs is the male DNA utilized, producing sons. We found that mixing of parental genomes only gives rise to males because the Y-bearing sperm of males are much more competent than the X-bearing sperm for penetrating the eggs. In this previously unrecognized strategy, asexual females produce few sexual males whose genes never reenter the female pool. Here, production of males is of interest only if sons are more likely to mate with their sisters. Using game theory, we show that in this context, the production of 9% males by M. belari females is an evolutionary stable strategy.
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Affiliation(s)
- Manon Grosmaire
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Caroline Launay
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Marion Siegwald
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Thibault Brugière
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Lilia Estrada-Virrueta
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Duncan Berger
- The Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Claire Burny
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France.,Present address: Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna A-1210, Austria
| | - Laurent Modolo
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Mark Blaxter
- The Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Marie-Anne Félix
- Département de Biologie, Ecole Normale Supérieure, IBENS, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Pierre-Henri Gouyon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Marie Delattre
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France.
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Coraggio F, Püschel R, Marti A, Meister P. Polycomb and Notch signaling regulate cell proliferation potential during Caenorhabditis elegans life cycle. Life Sci Alliance 2019; 2:e201800170. [PMID: 30599047 PMCID: PMC6306570 DOI: 10.26508/lsa.201800170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
Stable cell fate is an essential feature for multicellular organisms in which individual cells achieve specialized functions. Caenorhabditis elegans is a great model to analyze the determinants of cell fate stability because of its invariant lineage. We present a tractable cell fate challenge system that uses the induction of fate-specifying transcription factors. We show that wild-type differentiated animals are highly resistant to fate challenge. Removal of heterochromatin marks showed marked differences: the absence of histone 3 lysine 9 methylation (H3K9) has no effect on fate stability, whereas Polycomb homolog mes-2 mutants lacking H3K27 methylation terminally arrest larval development upon fate challenge. Unexpectedly, the arrest correlated with widespread cell proliferation rather than transdifferentiation. Using a candidate RNAi larval arrest-rescue screen, we show that the LIN-12Notch pathway is essential for hyperplasia induction. Moreover, Notch signaling appears downstream of food-sensing pathways, as dauers and first larval stage diapause animals are resistant to fate challenge. Our results demonstrate an equilibrium between proliferation and differentiation regulated by Polycomb and Notch signaling in the soma during the nematode life cycle.
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Affiliation(s)
- Francesca Coraggio
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ringo Püschel
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Alisha Marti
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
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Meister P, Kelker W, Gößler U, Hammerstingl R, Vogl TJ, Winkelmann R. [Vascularized tumor of the retroauricular skin]. Pathologe 2018; 39:330-332. [PMID: 29789864 DOI: 10.1007/s00292-018-0445-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An 84-year-old female patient with loss of hearing and otorrhoea went to an otolaryngologist. On examination, a polypoid mass in the auditory canal and a retroauricular skin lesion, possibly seborrheic keratosis, were found. Only the skin was submitted for histological examination and showed a cutaneous highly vascular lesion with an associated "zellballen" of clear cells without atypia. The initial diagnosis was that of a cutaneous glomangioma. Immunohistochemical findings favored diagnosis of a paraganglioma. Additional clinical information revealed a large mastoid tumor mass. Therefore, the findings were compatible with an jugulotympanic paraganglioma with infiltration of the overlying skin. This possibility was initially not considered in differential diagnosis, as cutaneous glomangiomas are relatively common (typically located on the hands). Cutaneous paragangliomas, however, are not reported.
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Affiliation(s)
- P Meister
- Dr. Senckenbergisches Institut für Pathologie, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 6, 60590, Frankfurt am Main, Deutschland
| | - W Kelker
- St. Marienkrankenhaus, Frankfurt am Main, Deutschland
| | - U Gößler
- St. Marienkrankenhaus, Frankfurt am Main, Deutschland
| | - R Hammerstingl
- Institut für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland
| | - T J Vogl
- Institut für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland
| | - R Winkelmann
- Dr. Senckenbergisches Institut für Pathologie, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 6, 60590, Frankfurt am Main, Deutschland.
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Meister P. [Report on the dermatopathology working group meeting : 101st anniversary of the DGP, Erlangen 24.06.2017]. Pathologe 2017; 38:218-219. [PMID: 28879380 DOI: 10.1007/s00292-017-0334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- P Meister
- , Hesseloherstr. 8, 80802, München, Deutschland.
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Abstract
Three paratracheal lymph nodes of a 20-year-old patient were submitted for examination, of which one showed numerous thyrocytes with large void nuclei and was suspected of being metastatic papillary thyroid carcinoma. The simultaneously resected thyroid gland, which was subsequently submitted showed findings consistent with Hashimoto's autoimmune thyroiditis (AIT). In the context of the resected goiter tissue, the suspected lymph node metastasis was identified as a hyperplastic ectopic (so-called parasitic) goiter nodule with thyrocytic changes typically seen in Hashimoto's AIT, such as oxyphilic cell alterations and a high plasma cell content. The re-examination of the suspicious lymph node revealed complete lack of a marginal sinus, thus excluding the diagnosis of a lymph node as well as the diagnosis of thyroid carcinoma metastasis.
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Affiliation(s)
- P Meister
- Dr. Senckenbergisches Institut für Pathologie, Klinikum der J. W. Goethe Universität Frankfurt am Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland
| | - C Vorländer
- Endokrine Chirurgie, Bürgerhospital, Nibelungenallee, Frankfurt am Main, Deutschland
| | - S Hartmann
- Dr. Senckenbergisches Institut für Pathologie, Klinikum der J. W. Goethe Universität Frankfurt am Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland.
| | - M-L Hansmann
- Dr. Senckenbergisches Institut für Pathologie, Klinikum der J. W. Goethe Universität Frankfurt am Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland
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Jost D, Vaillant C, Meister P. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr Opin Cell Biol 2016; 44:20-27. [PMID: 28040646 DOI: 10.1016/j.ceb.2016.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 07/27/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/17/2022]
Abstract
Over the past decade, advances in molecular methods have strikingly improved the resolution at which nuclear genome folding can be analyzed. This revealed a wealth of conserved features organizing the one dimensional DNA molecule into tridimensional nuclear domains. In this review, we briefly summarize the main findings and highlight how models based on polymer physics shed light on the principles underlying the formation of these domains. Finally, we discuss the mechanistic similarities allowing self-organization of these structures and the functional importance of these in the maintenance of transcriptional programs.
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Affiliation(s)
- Daniel Jost
- University Grenoble Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, F-38706 La Tronche, France
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69007 Lyon, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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12
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Sharma R, Ritler D, Meister P. Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development. Genesis 2016; 54:151-9. [PMID: 26845390 DOI: 10.1002/dvg.22925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/06/2022]
Abstract
C. elegans has recently emerged as a valuable model to understand the link between nuclear organization and cell fate, by combining microscopy approaches, genome-wide mapping techniques with advanced genetics. Crucial to these analyses are techniques to determine the genome-wide interaction pattern of proteins with DNA. Chromatin immunoprecipitation has proven valuable but it requires considerable amounts of starting material. This is sometimes difficult to achieve, in particular for specific genotypes (balanced strains, different sexes, severe phenotypes…). As an alternative to ChIP, DNA adenine methyltransferase identification by sequencing (DamID-seq) was recently shown to be able to characterize binding sites in single mammalian cells. Additionally, DamID can be achieved for cell-type specific analysis by expressing Dam fusion proteins under tissue specific promoters in a controlled manner. In this report, we present a user-friendly pipeline to analyse DamID-seq data in C. elegans. Based upon this pipeline, we provide a comparative analysis of libraries generated with different starting material and discuss important library features. Moreover, we introduce an adaptation of an imaging based tool to visualize in vivo the cell-specific tridimensional binding pattern of any protein of interest.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Dominic Ritler
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland
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13
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Meister P. [Report of the Dermatopathology Working Group : Berlin 2016]. Pathologe 2016; 37:229-230. [PMID: 27613299 DOI: 10.1007/s00292-016-0192-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- P Meister
- , Hesseloher Str. 8, 80802, München, Deutschland.
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Abstract
The existence of different domains within the nucleus has been clear from the time, in the late 1920s, that heterochromatin and euchromatin were discovered. The observation that heterochromatin is less transcribed than euchromatin suggested that microscopically identifiable structures might correspond to functionally different domains of the nucleus. Until 15 years ago, studies linking gene expression and subnuclear localization were limited to a few genes. As we discuss in this Review, new genome-wide techniques have now radically changed the way nuclear organization is analyzed. These have provided a much more detailed view of functional nuclear architecture, leading to the emergence of a number of new paradigms of chromatin folding and how this folding evolves during development.
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Affiliation(s)
- Ringo Pueschel
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Francesca Coraggio
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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Sharma R, Meister P. Dosage compensation and nuclear organization: cluster to control chromosome-wide gene expression. Curr Opin Genet Dev 2016; 37:9-16. [PMID: 26748388 DOI: 10.1016/j.gde.2015.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/18/2015] [Accepted: 11/25/2015] [Indexed: 11/28/2022]
Abstract
In many species, male and female animals differ in the number of X chromosomes they possess. As a consequence, large scale differences in gene dosage exist between sexes; a phenomenon that is rarely tolerated by the organism for changes in autosome dosage. Several strategies have evolved independently to balance X-linked gene dosage between sexes, named dosage compensation (DC). The molecular basis of DC differs among the three best-studied examples: mammals, fruit fly and nematodes. In this short review, we summarize recent microscopic and chromosome conformation capture data that reveal key features of the compensated X chromosome and highlight the events leading to the establishment of a functional, specialized nuclear compartment, the X domain.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland.
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16
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Meister P. [Report of the working group on dermatopathology]. Pathologe 2015; 36 Suppl 2:216. [PMID: 26489642 DOI: 10.1007/s00292-015-0063-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P Meister
- , Hesseloher Str. 8, 80802, München, Deutschland.
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17
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Heckmann A, Meister P, Meyer HW, Rohrbach A, Winter M, Placke T. Synthesis of Spherical Graphite Particles and Their Application as Cathode Material in Dual-Ion Cells. ACTA ACUST UNITED AC 2015. [DOI: 10.1149/06611.0001ecst] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Abstract
Animal sex is determined by the number of X chromosomes in many species, creating unequal gene dosage (aneuploidy) between sexes. Dosage Compensation mechanisms equalize this dosage difference by regulating X-linked gene expression. In the nematode C. elegans the current model suggests that DC is achieved by a 2-fold transcriptional downregulation in hermaphrodites mediated by the Dosage Compensation Complex (DCC), which restricts access to RNA Polymerase II by an unknown mechanism. Taking a nuclear organization point of view, we showed that the male X chromosome resides in the pore proximal subnuclear compartment whereas the DCC bound to the X, inhibits this spatial organization in the hermaphrodites. Here we discuss our results and propose a model that reassigns the role of DCC from repression of genes to inhibition of activation.
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Affiliation(s)
- Rahul Sharma
- a Cell Fate and Nuclear Organization ; Institute of Cell Biology ; University of Bern ; Bern , Switzerland
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19
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Birgel D, Meister P, Lundberg R, Horath TD, Bontognali TRR, Bahniuk AM, de Rezende CE, Vasconcelos C, McKenzie JA. Methanogenesis produces strong 13C enrichment in stromatolites of Lagoa Salgada, Brazil: a modern analogue for Palaeo-/Neoproterozoic stromatolites? Geobiology 2015; 13:245-266. [PMID: 25773379 DOI: 10.1111/gbi.12130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Holocene stromatolites characterized by unusually positive inorganic δ(13) CPDB values (i.e. up to +16‰) are present in Lagoa Salgada, a seasonally brackish to hypersaline lagoon near Rio de Janeiro (Brazil). Such positive values cannot be explained by phototrophic fixation of CO2 alone, and they suggest that methanogenesis was a dominating process during the growth of the stromatolites. Indeed, up to 5 mm methane was measured in the porewater. The archaeal membrane lipid archaeol showing δ(13) C values between -15 and 0‰ suggests that archaea are present and producing methane in the modern lagoon sediment. Moreover, (13) C-depleted hopanoids diplopterol and 3β-methylated C32 17β(H),21β(H)-hopanoic acid (both -40‰) are preserved in lagoon sediments and are most likely derived from aerobic methanotrophic bacteria thriving in the methane-enriched water column. Loss of isotopically light methane through the water column would explain the residual (13) C-enriched pool of dissolved inorganic carbon from where the carbonate constituting the stromatolites precipitated. The predominance of methanogenic archaea in the lagoon is most likely a result of sulphate limitation, suppressing the activity of sulphate-reducing bacteria under brackish conditions in a seasonally humid tropical environment. Indeed, sulphate-reduction activity is very low in the modern sediments. In absence of an efficient carbonate-inducing metabolic process, we propose that stromatolite formation in Lagoa Salgada was abiotically induced, while the (13) C-enriched organic and inorganic carbon pools are due to methanogenesis. Unusually, (13) C-enriched stromatolitic deposits also appear in the geological record of prolonged periods in the Palaeo- and Neoproterozoic. Lagoa Salgada represents a possible modern analogue to conditions that may have been widespread in the Proterozoic, at times when low sulphate concentrations in sea water allowed methanogens to prevail over sulphate-reducing bacteria.
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Affiliation(s)
- D Birgel
- Department of Geodynamics and Sedimentology, University of Vienna, Vienna, Austria
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20
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Meister P. [History of dermatopathology]. Pathologe 2015; 36:7-10. [PMID: 25663184 DOI: 10.1007/s00292-014-2053-5] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hebra in Vienna and later Unna in Hamburg are considered to be the protagonists of academic dermatopathology in the German-speaking literature. Whereas the former used a chiefly macroscopic approach to an academic classification, the concepts of the latter were based on microscopic observations. In contrast to pathologists, who in the nineteenth century were dominated by Virchow and his teachings, dermatologists as well as microscopically active gynecologists already applied histological findings for diagnostics and subsequent therapy. Chapters dealing with diseases of the skin in multivolume handbooks of pathology were initially mainly written by dermatologists. The majority of textbooks of dermatopathology were also written by dermatologists. One of the current aims of pathologists is the application of additional methods, e.g. molecular pathology in order to better understand and treat neoplastic diseases, in particular pigmented skin tumors.
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Affiliation(s)
- P Meister
- -, Hesseloherstr. 8, 80802, München, Deutschland,
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21
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Sharma R, Jost D, Kind J, Gómez-Saldivar G, van Steensel B, Askjaer P, Vaillant C, Meister P. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans. Genes Dev 2014; 28:2591-6. [PMID: 25452271 PMCID: PMC4248290 DOI: 10.1101/gad.248864.114] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 01/04/2023]
Abstract
The adjustment of X-linked gene expression to the X chromosome copy number (dosage compensation [DC]) has been widely studied as a model of chromosome-wide gene regulation. In Caenorhabditis elegans, DC is achieved by twofold down-regulation of gene expression from both Xs in hermaphrodites. We show that in males, the single X chromosome interacts with nuclear pore proteins, while in hermaphrodites, the DC complex (DCC) impairs this interaction and alters X localization. Our results put forward a structural model of DC in which X-specific sequences locate the X chromosome in transcriptionally active domains in males, while the DCC prevents this in hermaphrodites.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Daniel Jost
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, UMR 5672, Centre National de la Recherche Scientifique (CNRS), 69007 Lyon, France
| | - Jop Kind
- Division of Gene Regulation, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands
| | | | - Bas van Steensel
- Division of Gene Regulation, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands
| | - Peter Askjaer
- Spanish National Research Council (CSIC), The Junta of Andalusia (JA), Universidad Pablo de Olavide, Andalusian Center for Developmental Biology (CABD), 41013 Sevilla, Spain
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, UMR 5672, Centre National de la Recherche Scientifique (CNRS), 69007 Lyon, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland;
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22
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Meister P. [Report of the working group on dermatopathology 2014]. Pathologe 2014; 35 Suppl 2:281-2. [PMID: 25394978 DOI: 10.1007/s00292-014-1967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- P Meister
- -, Hesseloher Str. 8, 80802, München, Deutschland,
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23
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Bou Dib P, Gnägi B, Daly F, Sabado V, Tas D, Glauser DA, Meister P, Nagoshi E. A conserved role for p48 homologs in protecting dopaminergic neurons from oxidative stress. PLoS Genet 2014; 10:e1004718. [PMID: 25340742 PMCID: PMC4207665 DOI: 10.1371/journal.pgen.1004718] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 04/10/2014] [Accepted: 08/29/2014] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease (PD) is the most common neurodegenerative movement disorder characterized by the progressive loss of dopaminergic (DA) neurons. Both environmental and genetic factors are thought to contribute to the pathogenesis of PD. Although several genes linked to rare familial PD have been identified, endogenous risk factors for sporadic PD, which account for the majority of PD cases, remain largely unknown. Genome-wide association studies have identified many single nucleotide polymorphisms associated with sporadic PD in neurodevelopmental genes including the transcription factor p48/ptf1a. Here we investigate whether p48 plays a role in the survival of DA neurons in Drosophila melanogaster and Caenorhabditis elegans. We show that a Drosophila p48 homolog, 48-related-2 (Fer2), is expressed in and required for the development and survival of DA neurons in the protocerebral anterior medial (PAM) cluster. Loss of Fer2 expression in adulthood causes progressive PAM neuron degeneration in aging flies along with mitochondrial dysfunction and elevated reactive oxygen species (ROS) production, leading to the progressive locomotor deficits. The oxidative stress challenge upregulates Fer2 expression and exacerbates the PAM neuron degeneration in Fer2 loss-of-function mutants. hlh-13, the worm homolog of p48, is also expressed in DA neurons. Unlike the fly counterpart, hlh-13 loss-of-function does not impair development or survival of DA neurons under normal growth conditions. Yet, similar to Fer2, hlh-13 expression is upregulated upon an acute oxidative challenge and is required for the survival of DA neurons under oxidative stress in adult worms. Taken together, our results indicate that p48 homologs share a role in protecting DA neurons from oxidative stress and degeneration, and suggest that loss-of-function of p48 homologs in flies and worms provides novel tools to study gene-environmental interactions affecting DA neuron survival. Parkinson's disease is a common movement disorder with no known cure. Its characteristic motor symptoms are primarily caused by the progressive loss of midbrain dopaminergic neurons. Although studies have shown that various environmental and genetic factors both contribute to the development of the disease, the underlying mechanisms remain unknown. Here we use powerful invertebrate model organisms, fruit flies and nematode worms, and identify a new gene required for the survival of dopaminergic neurons. We show that homologs of the p48/ptf1-a gene in both flies and worms are expressed in dopaminergic neurons and mutations in p48 increase the susceptibility of dopaminergic neuron death when animals are under oxidative stress. Importantly, genetic variations in p48 in humans have been detected in the sporadic Parkinson's disease patients, indicating the possibility that similar mechanism might play a role in the death of dopaminergic neurons in humans. Oxidative stress has been regarded as a major pathogenic factor for Parkinson's disease. Our results add evidence to the link between oxidative stress and neurodegeneration, and suggest that p48 mutant flies and worms can be used to study mechanisms of neurodegeneration in Parkinson's disease.
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Affiliation(s)
- Peter Bou Dib
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Gnägi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Fiona Daly
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Virginie Sabado
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Damla Tas
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Dominique A. Glauser
- Department of Biology/Zoology, University of Fribourg, Chemin du Musée, Fribourg, Switzerland
| | - Peter Meister
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Emi Nagoshi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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Abstract
In recent years, Caenorhabditis elegans has emerged as a new model to investigate the relationships between nuclear architecture, cellular differentiation, and organismal development. On one hand, C. elegans with its fixed lineage and transparent body is a great model organism to observe gene functions in vivo in specific cell types using microscopy. On the other hand, two different techniques have been applied in nematodes to identify binding sites for chromatin-associated proteins genome-wide: chromatin immunoprecipitation (ChIP), and Dam-mediated identification (DamID). We summarize here all three techniques together as they are complementary. We also highlight strengths and differences of the individual approaches.
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Affiliation(s)
- Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain.
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25
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Askjaer P, Galy V, Meister P. Modern Tools to Study Nuclear Pore Complexes and Nucleocytoplasmic Transport in Caenorhabditis elegans. Methods Cell Biol 2014; 122:277-310. [DOI: 10.1016/b978-0-12-417160-2.00013-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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26
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Meister P, Moll I. [Report of the Working Group on Dermatopathology at the 97th annual meeting of the DGP in Heidelberg]. Pathologe 2013; 34 Suppl 2:282-3. [PMID: 24196630 DOI: 10.1007/s00292-013-1868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P Meister
- -, Hesseloher Str. 8, 80802, München, Deutschland,
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Rohner S, Kalck V, Wang X, Ikegami K, Lieb JD, Gasser SM, Meister P. Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans. ACTA ACUST UNITED AC 2013; 200:589-604. [PMID: 23460676 PMCID: PMC3587839 DOI: 10.1083/jcb.201207024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The hsp-16.2 promoter is sufficient for recruitment of hsp-16.2 to nuclear pore complexes in a manner dependent on RNA pol II and ENY-2, but not on full-length mRNA production. Some inducible yeast genes relocate to nuclear pores upon activation, but the general relevance of this phenomenon has remained largely unexplored. Here we show that the bidirectional hsp-16.2/41 promoter interacts with the nuclear pore complex upon activation by heat shock in the nematode Caenorhabditis elegans. Direct pore association was confirmed by both super-resolution microscopy and chromatin immunoprecipitation. The hsp-16.2 promoter was sufficient to mediate perinuclear positioning under basal level conditions of expression, both in integrated transgenes carrying from 1 to 74 copies of the promoter and in a single-copy genomic insertion. Perinuclear localization of the uninduced gene depended on promoter elements essential for induction and required the heat-shock transcription factor HSF-1, RNA polymerase II, and ENY-2, a factor that binds both SAGA and the THO/TREX mRNA export complex. After induction, colocalization with nuclear pores increased significantly at the promoter and along the coding sequence, dependent on the same promoter-associated factors, including active RNA polymerase II, and correlated with nascent transcripts.
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Affiliation(s)
- Sabine Rohner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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Abstract
With its invariant cell lineage, easy genetics and small genome, the nematode Caenorhabditis elegans has emerged as one of the prime models in developmental biology over the last 50 years. Surprisingly however, until a decade ago very little was known about nuclear organization in worms, even though it is an ideal model system to explore the link between nuclear organization and cell fate determination. Here, we review the latest findings that exploit the repertoire of genetic tools developed in worms, leading to the identification of important sequences and signals governing the changes in chromatin tridimensional architecture. We also highlight parallels and differences to other model systems.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
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29
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Meister P, Taddei A. Building silent compartments at the nuclear periphery: a recurrent theme. Curr Opin Genet Dev 2013; 23:96-103. [PMID: 23312840 DOI: 10.1016/j.gde.2012.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 01/12/2023]
Abstract
In eukaryotes, the genetic material is stored in the nucleus, which is enclosed in a double lipid bilayer, the nuclear envelope (NE). It protects the genome from physical stress and separates it from the rest of the cell. On top of this physical function, growing evidence shows that the nuclear periphery contributes to the 3D organization of the genome. In turn, tridimensional organization of chromatin in the nuclear space influences genome expression. Here we review recent findings on the function of this physical barrier in gene repression and latest models on how silent subnuclear compartments at the NE are built in yeast as well as in the nematode C. elegans and mammalian cells; trying to draw parallels between the three systems.
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Affiliation(s)
- Peter Meister
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland.
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Abstract
During development, the genome undergoes drastic reorganization within the nuclear space. To determine tridimensional genome folding, genome-wide techniques (damID/Hi-C) can be applied using cell populations, but these have to be calibrated using microscopy and single-cell analysis of gene positioning. Moreover, the dynamic behavior of chromatin has to be assessed on living samples. Combining fast stereotypic development with easy genetics and microscopy, the nematode C. elegans has become a model of choice in recent years to study changes in nuclear organization during cell fate acquisition. Here we present two complementary techniques to evaluate nuclear positioning of genes either by fluorescence in situ hybridization in fixed samples or in living worm embryos using the GFP-lacI/lacO chromatin-tagging system.
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Affiliation(s)
- Christian Lanctôt
- First Faculty of Medicine, Institute of Cellular Biology and Pathology, Charles University in Prague, Prague, Czech Republic
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Allan J, Clifford A, Ball P, Alston M, Meister P. 'You're less complete if you haven't got a can in your hand': alcohol consumption and related harmful effects in rural Australia: the role and influence of cultural capital. Alcohol Alcohol 2012; 47:624-9. [PMID: 22763230 DOI: 10.1093/alcalc/ags074] [Citation(s) in RCA: 35] [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: 11/13/2022] Open
Abstract
AIMS This study aimed to explore rural Australians' perceptions of social and cultural factors influencing alcohol use in their communities. METHODS Semi-structured interviews exploring rural community key informants' (n = 46) perceptions of social and cultural factors influencing alcohol consumption in their community were conducted. A narrative analysis identified cultural capital as a salient concept for explaining how rural community life is created and sustained via drinking practices. RESULTS Themes relating to participants' accounts of learning to drink, normal drinking; exclusion because of not drinking and problematic drinkers are described. CONCLUSION In rural communities, beliefs and values about drinking as a positive social practice are transmitted, rewarded and reproduced across multiple groups and settings, reinforcing that drinking is an integral part of Australian rural culture. Drinking is so important that engaging in drinking practices creates and sustains cultural capital. As a result, alcohol-related harm is of little concern to rural dwellers.
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Affiliation(s)
- Julaine Allan
- The Lyndon Community, PO Box 9374, Orange, NSW 2800, Australia.
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Meister P, Schott S, Bedet C, Xiao Y, Rohner S, Bodennec S, Hudry B, Molin L, Solari F, Gasser SM, Palladino F. Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism. Genome Biol 2011; 12:R123. [PMID: 22185090 PMCID: PMC3334618 DOI: 10.1186/gb-2011-12-12-r123] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 11/30/2011] [Accepted: 12/20/2011] [Indexed: 01/23/2023] Open
Abstract
Background Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP1 homolog HPL-2 at specific developmental stages. Results We show that HPL-2 regulates the expression of germline genes, extracellular matrix components and genes involved in lipid metabolism. Comparison of our expression data with HPL-2 ChIP-on-chip profiles reveals that a significant number of genes up- and down-regulated in the absence of HPL-2 are bound by HPL-2. Germline genes are specifically up-regulated in hpl-2 mutants, consistent with the function of HPL-2 as a repressor of ectopic germ cell fate. In addition, microarray results and phenotypic analysis suggest that HPL-2 regulates the dauer developmental decision, a striking example of phenotypic plasticity in which environmental conditions determine developmental fate. HPL-2 acts in dauer at least partly through modulation of daf-2/IIS and TGF-β signaling pathways, major determinants of the dauer program. hpl-2 mutants also show increased longevity and altered lipid metabolism, hallmarks of the long-lived, stress resistant dauers. Conclusions Our results suggest that the worm HP1 homologue HPL-2 may coordinately regulate dauer diapause, longevity and lipid metabolism, three processes dependent on developmental input and environmental conditions. Our findings are of general interest as a paradigm of how chromatin factors can both stabilize development by buffering environmental variation, and guide the organism through remodeling events that require plasticity of cell fate regulation.
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Affiliation(s)
- Peter Meister
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon, Ecole Normale Supérieure, Lyon Cedex 07, France
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Meister P. [Minutes of the meeting of the Working Group on Dermapathology: Leipzig 16 June 2011]. Pathologe 2011; 32 Suppl 2:337-338. [PMID: 22033688 DOI: 10.1007/s00292-011-1483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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34
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Mattout A, Pike BL, Towbin BD, Bank EM, Gonzalez-Sandoval A, Stadler MB, Meister P, Gruenbaum Y, Gasser SM. An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity. Curr Biol 2011; 21:1603-14. [PMID: 21962710 DOI: 10.1016/j.cub.2011.08.030] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/30/2011] [Accepted: 08/12/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND In worms, as in other organisms, many tissue-specific promoters are sequestered at the nuclear periphery when repressed and shift inward when activated. It has remained unresolved, however, whether the association of facultative heterochromatin with the nuclear periphery, or its release, has functional relevance for cell or tissue integrity. RESULTS Using ablation of the unique lamin gene in C. elegans, we show that lamin is necessary for the perinuclear positioning of heterochromatin. We then express at low levels in otherwise wild-type worms a lamin carrying a point mutation, Y59C, which in humans is linked to an autosomal-dominant form of Emery-Dreifuss muscular dystrophy. Using embryos and differentiated tissues, we track the subnuclear position of integrated heterochromatic arrays and their expression. In LMN-1 Y59C-expressing worms, we see abnormal retention at the nuclear envelope of a gene array bearing a muscle-specific promoter. This correlates with impaired activation of the array-borne myo-3 promoter and altered expression of a number of muscle-specific genes. However, an equivalent array carrying the intestine-specific pha-4 promoter is expressed normally and shifts inward when activated in gut cells of LMN-1 Y59C worms. Remarkably, adult LMN-1 Y59C animals have selectively perturbed body muscle ultrastructure and reduced muscle function. CONCLUSION Lamin helps sequester heterochromatin at the nuclear envelope, and wild-type lamin permits promoter release following tissue-specific activation. A disease-linked point mutation in lamin impairs muscle-specific reorganization of a heterochromatic array during tissue-specific promoter activation in a dominant manner. This dominance and the correlated muscle dysfunction in LMN-1 Y59C worms phenocopies Emery-Dreifuss muscular dystrophy.
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Affiliation(s)
- Anna Mattout
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Towbin BD, Meister P, Pike BL, Gasser SM. Repetitive transgenes in C. elegans accumulate heterochromatic marks and are sequestered at the nuclear envelope in a copy-number- and lamin-dependent manner. Cold Spring Harb Symp Quant Biol 2011; 75:555-65. [PMID: 21467137 DOI: 10.1101/sqb.2010.75.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chromatin is nonrandomly distributed in nuclear space, yet the functional significance of this remains unclear. Here, we make use of transgenes carrying developmentally regulated promoters to study subnuclear gene positioning during the development of Caenorhabditis elegans. We found that small transgenes (copy number ≤50) are randomly distributed in early embryonic nuclei, independent of promoter activity. However, in differentiated tissues, these same transgenes occupied specific subnuclear positions: When promoters are repressed, transgenes are found at the nuclear periphery, whereas active, developmentally regulated promoters are enriched in the nuclear core. The absence of specific transgene positioning in embryonic nuclei does not reflect an absence of proteins that mediate perinuclear sequestration: Embryonic nuclei are able to sequester much larger transgene arrays (copy number 300-500) at the periphery. This size-dependent peripheral positioning of gene arrays in early embryos correlates with the accumulation of heterochromatic marks (H3K9me3 and H3K27me3) on large arrays. Interestingly, depletion of nuclear lamina components caused release of arrays from the nuclear envelope and interfered with their efficient silencing. Our results suggest that developmentally silenced chromatin binds the nuclear lamina in a manner correlated with the deposition of heterochromatic marks. Peripheral sequestration of chromatin may, in turn, support the maintenance of silencing.
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Affiliation(s)
- B D Towbin
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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36
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Meister P, Mango SE, Gasser SM. Locking the genome: nuclear organization and cell fate. Curr Opin Genet Dev 2011; 21:167-74. [PMID: 21345665 DOI: 10.1016/j.gde.2011.01.023] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/28/2011] [Accepted: 01/28/2011] [Indexed: 01/12/2023]
Abstract
The differentiation of pluripotent or totipotent cells into various differentiated cell types is accompanied by a restriction of gene expression patterns, alteration in histone and DNA methylation, and changes in the gross nuclear organization of eu- and heterochromatic domains. Several recent studies have coupled genome-wide mapping of histone modifications with changes in gene expression. Other studies have examined changes in the subnuclear positioning of tissue-specific genes upon transcriptional induction or repression. Here we summarize intriguing correlations of the three phenomena, which suggest that in some cases causal relationships may exist.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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Gehlen LR, Nagai S, Shimada K, Meister P, Taddei A, Gasser SM. Nuclear geometry and rapid mitosis ensure asymmetric episome segregation in yeast. Curr Biol 2010; 21:25-33. [PMID: 21194950 DOI: 10.1016/j.cub.2010.12.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/10/2010] [Accepted: 12/08/2010] [Indexed: 11/20/2022]
Abstract
BACKGROUND Asymmetric cell division drives the generation of differentiated cells and maintenance of stem cells. In budding yeast, autonomously replicating sequence (ARS) plasmids lacking centromere elements are asymmetrically segregated into the mother cell, where they are thought to contribute to cellular senescence. This phenomenon has been proposed to result from the active retention of plasmids through an interaction with nuclear pores. RESULTS To investigate the mother-daughter segregation bias of plasmids, we used live-cell imaging to follow the behavior of extrachromosomal DNA. We show that both an excised DNA ring and a centromere-deficient ARS plasmid move freely in the nucleoplasm yet show a strong segregation bias for the mother cell. Computational modeling shows that the geometrical shape of the dividing yeast nucleus and length of mitosis severely restrict the passive diffusion of episomes into daughter nuclei. Predictions based on simulated nuclear division were tested with mutants that extend the length of mitosis. Finally, explaining how various anchors can improve mitotic segregation, we show that plasmid partitioning is improved by tethering the plasmid to segregating structures, such as the nuclear envelope and telomeres. CONCLUSIONS The morphology and brevity of mitotic division in budding yeast impose physical constraints on the diffusion of material into the daughter, obviating the need for a retention mechanism to generate rejuvenated offspring.
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Affiliation(s)
- Lutz R Gehlen
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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Kiene H, Brinkhaus B, Fischer G, Girke M, Hahn E, Hoppe H, Jütte R, Kraft K, Klitzsch W, Matthiessen P, Meister P, Michalsen A, Teut M, Willich S, Heimpel H. Professional treatment in the context of medical pluralism—A German perspective. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM. The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev 2010; 24:766-82. [PMID: 20395364 PMCID: PMC2854392 DOI: 10.1101/gad.559610] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/25/2010] [Indexed: 12/23/2022]
Abstract
To understand whether the spatial organization of the genome reflects the cell's differentiated state, we examined whether genes assume specific subnuclear positions during Caenorhabditis elegans development. Monitoring the radial position of developmentally controlled promoters in embryos and larval tissues, we found that small integrated arrays bearing three different tissue-specific promoters have no preferential position in nuclei of undifferentiated embryos. However, in differentiated cells, they shifted stably toward the nuclear lumen when activated, or to the nuclear envelope when silent. In contrast, large integrated arrays bearing the same promoters became heterochromatic and nuclear envelope-bound in embryos. Tissue-specific activation of promoters in these large arrays in larvae overrode the perinuclear anchorage. For transgenes that carry both active and inactive promoters, the inward shift of the active promoter was dominant. Finally, induction of master regulator HLH-1 prematurely induced internalization of a muscle-specific promoter array in embryos. Fluorescence in situ hybridization confirmed analogous results for the endogenous endoderm-determining gene pha-4. We propose that, in differentiated cells, subnuclear organization arises from the selective positioning of active and inactive developmentally regulated promoters. We characterize two forces that lead to tissue-specific subnuclear organization of the worm genome: large repeat-induced heterochromatin, which associates with the nuclear envelope like repressed genes in differentiated cells, and tissue-specific promoters that shift inward in a dominant fashion over silent promoters, when they are activated.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Benjamin D. Towbin
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Brietta L. Pike
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Aaron Ponti
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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40
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Abstract
We describe here optimized protocols for tagging genomic DNA sequences with bacterial operator sites to enable visualization of specific loci in living budding yeast cells. Quantitative methods for the analysis of locus position relative to the nuclear center or nuclear pores, the analysis of chromatin dynamics and the relative position of tagged loci to other nuclear landmarks are described. Methods for accurate immunolocalization of nuclear proteins without loss of three-dimensional structure, in combination with fluorescence in situ hybridization, are also presented. These methods allow a robust analysis of subnuclear organization of both proteins and DNA in intact yeast cells.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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41
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Meister P. [Minutes of the meeting of the Dermatopathology Working Group]. Pathologe 2009; 30 Suppl 2:221. [PMID: 19756612 DOI: 10.1007/s00292-009-1198-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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42
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Towbin BD, Meister P, Gasser SM. The nuclear envelope--a scaffold for silencing? Curr Opin Genet Dev 2009; 19:180-6. [PMID: 19303765 DOI: 10.1016/j.gde.2009.01.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 01/23/2009] [Accepted: 01/27/2009] [Indexed: 01/19/2023]
Abstract
An increasing number of studies indicate that chromosomes are spatially organized in the interphase nucleus and that some genes tend to occupy characteristic zones of the nuclear volume. FISH studies in mammalian cells suggest a differential localization of active and inactive loci, with inactive heterochromatin being largely perinuclear. Recent genome-wide mapping techniques confirm that the nuclear lamina, which lies beneath the nuclear envelope, interacts preferentially with silent genes. To address the functional significance of spatial compartmentation, gain-of-function assays in which chromatin is targeted to the nuclear periphery have now been carried out. Such experiments yielded coherent models in yeast; however, conflicting results in mammalian cells leave it unclear whether these concepts apply to higher organisms. Nevertheless, the recent discovery that evolutionarily conserved inner nuclear membrane proteins support the peripheral anchoring of yeast heterochromatin suggests that certain principles of nuclear organization may hold true from yeast to man.
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Affiliation(s)
- Benjamin D Towbin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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Meister P. [Report of the dermatopathology working group]. Pathologe 2008; 29 Suppl 2:370. [PMID: 18853163 DOI: 10.1007/s00292-008-1084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Abstract
We describe a straightforward two-step PCR-based method to insert arrays of lac or tet operators (lacO or tetO) at specific loci in the budding yeast genome. The method entails insertion of a marker generated by PCR with classical long primers recognizing the locus of interest, followed by the replacement of this marker by a linearized plasmid bearing an array of lacI- or tetR-binding motifs. Using this technique, loci located either in the yeast genome or on yeast artificial chromosomes can be efficiently tagged. We provide a set of plasmids with different markers for cloning-free integration of lacO or tetO repeats into the yeast genome.
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Affiliation(s)
- Sabine Rohner
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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45
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Meister P. [Residual cancer or not residual cancer--that is the question]. Pathologe 2007; 28:308-11. [PMID: 17605065 DOI: 10.1007/s00292-007-0919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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46
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Meister P, Taddei A, Ponti A, Baldacci G, Gasser SM. Replication foci dynamics: replication patterns are modulated by S-phase checkpoint kinases in fission yeast. EMBO J 2007; 26:1315-26. [PMID: 17304223 PMCID: PMC1817620 DOI: 10.1038/sj.emboj.7601538] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 12/11/2006] [Indexed: 12/22/2022] Open
Abstract
Although the molecular enzymology of DNA replication is well characterised, how and why it occurs in discrete nuclear foci is unclear. Using fission yeast, we show that replication takes place in a limited number of replication foci, whose distribution changes with progression through S phase. These sites define replication factories which contain on average 14 replication forks. We show for the first time that entire foci are mobile, able both to fuse and re-segregate. These foci form distinguishable patterns during S phase, whose succession is reproducible, defining early-, mid- and late-S phase. In wild-type cells, this same temporal sequence can be detected in the presence of hydroxyurea (HU), despite the reduced rate of replication. In cells lacking the intra-S checkpoint kinase Cds1, replication factories dismantle on HU. Intriguingly, even in the absence of DNA damage, the replication foci in cds1 cells assume a novel distribution that is not present in wild-type cells, arguing that Cds1 kinase activity contributes to the spatio-temporal organisation of replication during normal cell growth.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- UMR2027, CNRS/Institut Curie, Bâtiment 110, Centre Universitaire, Orsay Cedex, France
| | - Angela Taddei
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- UMR218, CNRS/Institut Curie, 26 rue d'Ulm, Paris, France
| | - Aaron Ponti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Giuseppe Baldacci
- UMR2027, CNRS/Institut Curie, Bâtiment 110, Centre Universitaire, Orsay Cedex, France
- These authors contributed equally to this work
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- These authors contributed equally to this work
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. Tel.: +41 61 697 7255; Fax +41 61 697 6862; E-mail:
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Abstract
In this issue of Cell, use live-fluorescence microscopy to monitor individual genomic loci as they replicate in budding yeast. They confirm that DNA is recruited to replication factories and show that sister replication forks initiated from the same origin are held together within a single replication factory.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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Meister P, Taddei A, Vernis L, Poidevin M, Gasser SM, Baldacci G. Temporal separation of replication and recombination requires the intra-S checkpoint. ACTA ACUST UNITED AC 2005; 168:537-44. [PMID: 15716375 PMCID: PMC2171758 DOI: 10.1083/jcb.200410006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In response to DNA damage and replication pausing, eukaryotes activate checkpoint pathways that prevent genomic instability by coordinating cell cycle progression with DNA repair. The intra-S-phase checkpoint has been proposed to protect stalled replication forks from pathological rearrangements that could result from unscheduled recombination. On the other hand, recombination may be needed to cope with either stalled forks or double-strand breaks resulting from hydroxyurea treatment. We have exploited fission yeast to elucidate the relationship between replication fork stalling, loading of replication and recombination proteins onto DNA, and the intra-S checkpoint. Here, we show that a functional recombination machinery is not essential for recovery from replication fork arrest and instead can lead to nonfunctional fork structures. We find that Rad22-containing foci are rare in S-phase cells, but peak in G2 phase cells after a perturbed S phase. Importantly, we find that the intra-S checkpoint is necessary to avoid aberrant strand-exchange events during a hydroxyurea block.
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Affiliation(s)
- Peter Meister
- CNRS UMR2027, Institut Curie, Centre Universitaire, 91405 Orsay Cedex, France
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Abstract
The entity and nosology of pleomorphic malignant fibrous histiocytoma (MFH) is still ambiguous. The actual WHO-Classification uses pleomorphic malignant fibrous histiocytoma (MFH) and pleomorphic sarcoma NOS (not otherwise specified) synonymously. On the other hand text and illustrations convey the impression, that these tumors also could be pleomorphic lipo-, leio- or rhabdomyosarcomas etc. It would have been more informative to emphasize, that with the above mentioned specific sarcoma types MFH-like appearance may occur. Furthermore it would have been more up to date to consider pleomorphic sarcomas NOS as pleomorphic fibrosarcomas and include them in the chapter of fibroblastic and myofibroblastic tumors. This concept already has been carried out for the former myxoid variant of MFH, nowadays preferentially called myxofibrosarcoma. There is controversial discussion about the clinical significance of exact typing of pleomorphic sarcomas. Problems may also occur due to the lack of standards, which degree of desmin expression signifies leiomyosarcoma or just indicates myofibroblasts in MFH. The requirement of exclusion of other tumor-types before diagnosing pleomorphic fibrosarcoma still remains obligatory. After verification of the diagnosis pleomorphic sarcoma NOS or pleomorphic fibrosarcoma, grading e.g. according to criteria of the FFCCS can be carried out. Most cases of pleomorphic fibrosarcoma will qualify as high grade malignant.
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50
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Abstract
Histological grading according to one of the proven systems, e.g. that of the FFCCS, leads to the definition of different prognostic risk groups. Prerequisite is a precise typing of the tumors, if necessary by immunohistochemical and molecular-pathological methods. The therapeutic decision is dependent on the presence either of a low- or high-grade malignant tumor: With low-grade sarcomas surgery has priority, with high grade tumors usually chemo- and/or radiotherapy are indicated. With the latter, also better therapeutic response is reported. Therefore, conversion of a 3-grade into a 2-grade system has to be carried out by including the tumor localization as prognostic parameter. Thereby, the large group of G2-sarcomas with intermediate malignancy can be stratified. Superficial G2-sarcomas are considered to be low grade and deep G2-sarcomas high grade malignant. Immunohistochemical staining of tumor cell nuclei with Ki67/MIB1 allows a more standardized and precise grading. The ultimate aim, not to define risk groups, but to predict the prognosis for individual patients, possibly could be reached someday by molecular diagnostic methods.
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