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Ungethüm K, Wiedmann S, Wagner M, Leyh R, Ertl G, Frantz S, Geisler T, Karmann W, Prondzinsky R, Herdeg C, Noutsias M, Ludwig T, Käs J, Klocke B, Krapp J, Wood D, Kotseva K, Störk S, Heuschmann PU. Secondary prevention in diabetic and nondiabetic coronary heart disease patients: Insights from the German subset of the hospital arm of the EUROASPIRE IV and V surveys. Clin Res Cardiol 2023; 112:285-298. [PMID: 36166067 PMCID: PMC9898414 DOI: 10.1007/s00392-022-02093-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/25/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients with coronary heart disease (CHD) with and without diabetes mellitus have an increased risk of recurrent events requiring multifactorial secondary prevention of cardiovascular risk factors. We compared prevalences of cardiovascular risk factors and its determinants including lifestyle, pharmacotherapy and diabetes mellitus among patients with chronic CHD examined within the fourth and fifth EUROASPIRE surveys (EA-IV, 2012-13; and EA-V, 2016-17) in Germany. METHODS The EA initiative iteratively conducts European-wide multicenter surveys investigating the quality of secondary prevention in chronic CHD patients aged 18 to 79 years. The data collection in Germany was performed during a comprehensive baseline visit at study centers in Würzburg (EA-IV, EA-V), Halle (EA-V), and Tübingen (EA-V). RESULTS 384 EA-V participants (median age 69.0 years, 81.3% male) and 536 EA-IV participants (median age 68.7 years, 82.3% male) were examined. Comparing EA-IV and EA-V, no relevant differences in risk factor prevalence and lifestyle changes were observed with the exception of lower LDL cholesterol levels in EA-V. Prevalence of unrecognized diabetes was significantly lower in EA-V as compared to EA-IV (11.8% vs. 19.6%) while the proportion of prediabetes was similarly high in the remaining population (62.1% vs. 61.0%). CONCLUSION Between 2012 and 2017, a modest decrease in LDL cholesterol levels was observed, while no differences in blood pressure control and body weight were apparent in chronic CHD patients in Germany. Although the prevalence of unrecognized diabetes decreased in the later study period, the proportion of normoglycemic patients was low. As pharmacotherapy appeared fairly well implemented, stronger efforts towards lifestyle interventions, mental health programs and cardiac rehabilitation might help to improve risk factor profiles in chronic CHD patients.
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Affiliation(s)
- K Ungethüm
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany.
| | - S Wiedmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Berlin, Germany
| | - M Wagner
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Kuratorium für Dialyse und Nierentransplantation E.V, Neu-Isenburg, Hesse, Germany
| | - R Leyh
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
| | - G Ertl
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
| | - S Frantz
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Department of Internal Medicine III, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt, Halle (Saale), Germany
| | - T Geisler
- Department of Cardiology and Cardiovascular Disease, University Hospital Tübingen, Tübingen, Baden-Württemberg, Germany
| | - W Karmann
- Department of Medicine, Klinik Kitzinger Land, Kitzingen, Bavaria, Germany
| | - R Prondzinsky
- Cardiology/Intensive Care Medicine, Carl Von Basedow Klinikum Merseburg, Merseburg, Saxony-Anhalt, Germany
| | - C Herdeg
- Medius Klinik Ostfildern-Ruit, Klinik für Innere Medizin, Herz- und Kreislauferkrankungen, Ostfildern-Ruit, Baden-Württemberg, Germany
| | - M Noutsias
- Department of Internal Medicine III, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt, Halle (Saale), Germany
- Department of Internal Medicine A, University Hospital Ruppin-Brandenburg (UKRB) of the Medical School of Brandenburg (MHB), Neuruppin, Brandenburg, Germany
| | - T Ludwig
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
| | - J Käs
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
| | - B Klocke
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
| | - J Krapp
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
| | - D Wood
- European Society of Cardiology, Sophia Antipolis, France
- Imperial College Healthcare NHS Trusts, London, UK
- National University of Ireland, Galway, Ireland
| | - K Kotseva
- European Society of Cardiology, Sophia Antipolis, France
- Imperial College Healthcare NHS Trusts, London, UK
- National University of Ireland, Galway, Ireland
| | - S Störk
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
| | - P U Heuschmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Bavaria, Germany
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
- Clinical Trial Center, University Hospital Würzburg, Würzburg, Bavaria, Germany
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Chan T, Bolinger C, Scott S, Du M, Poortman C, Koenitzer B, Athwal T, Shepard L, Slone RD, Dutta S, Zilko S, Dunleavey JM, Zenere G, Plummer J, Klocke B, Zinser C, Ahmad S, Brough DE, Shah RR, Sabzevari H. Abstract 2821: Incorporation of intrinsic checkpoint blockade enhances functionality of multigenic autologous UltraCAR-T® cells manufactured using non-viral gene delivery and rapid manufacturing process. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Current chimeric antigen receptor (CAR)-T manufacturing utilizes viral vectors and extensive ex vivo expansion at large central facilities leading to an exhausted CAR-T phenotype, high costs and long vein-to-vein times. While allogeneic CAR-T can reduce delays in patient treatment, they require extensive manipulation of donor cells, severe lymphodepletion and demonstrate short persistence limiting their therapeutic window.
The UltraCAR-T® platform is designed to overcome these limitations by utilizing non-viral multigene delivery and a rapid, decentralized manufacturing process without ex vivo activation or expansion of T cells. Patient’s own T cells are collected and manufactured at the medical center and re-infused one day after gene transfer.
Here we describe the next generation UltraCAR-T platform that addresses the inhibitory tumor microenvironment by incorporating a novel mechanism for intrinsic downregulation of one or more checkpoint inhibitor (CPI) genes. Our design achieves intrinsic CPI blockade without gene editing and is aimed at avoiding systemic toxicity and the high cost of combining CPI antibodies. Next generation UltraCAR-T cells simultaneously express CAR, membrane bound IL-15 (mbIL15), kill switch, and incorporate intrinsic CPI blockade.
To illustrate the ability of this platform, we designed exemplary non-viral transposons to generate UltraCAR-T cells against multiple tumor targets incorporating intrinsic blockade of either one (PD-1) or two (PD-1 and TIGIT) CPI genes. Healthy donor T cells were transfected using the UltraPorator™ electroporation system to manufacture UltraCAR-T cells without ex vivo activation or expansion. The co-expression of CAR, mbIL15 and kill switch was confirmed by flow cytometry and western blot. Activated UltraCAR-T showed significant reduction in CPI gene expression compared to control CAR-T cells lacking the CPI blockade and did not show unintended off-target activity. Downregulation of CPI gene(s) on UltraCAR-T enhanced cytotoxicity and inflammatory cytokine production, especially at low effector to target (E:T) cell ratios, when co-cultured with PD-L1+/CD155+ tumor cells. Single-cell cytokine proteomics showed significant increase in polyfunctionality of UltraCAR-T with intrinsic downregulation of CPI gene(s). In vivo, a single infusion of receptor tyrosine kinase-like orphan receptor 1 (ROR1)-specific UltraCAR-T with intrinsic PD-1 blockade resulted in rapid expansion, an increase in preferred T cell memory (TSCM/TCM) populations, and significantly improved overall survival of ROR1+ PD-L1+ tumor bearing mice.
These preclinical data highlight the improved efficacy of incorporating intrinsic CPI blockade in UltraCAR-T cells using non-viral gene delivery and an established rapid, decentralized manufacturing process.
Citation Format: Tim Chan, Cheryl Bolinger, Sean Scott, Mengyan Du, Carol Poortman, Byron Koenitzer, Taranjit Athwal, Lindsey Shepard, R. Daniel Slone, Shourik Dutta, Steven Zilko, James M. Dunleavey, Giorgio Zenere, Jacques Plummer, Bernward Klocke, Christian Zinser, Shamim Ahmad, Douglas E. Brough, Rutul R. Shah, Helen Sabzevari. Incorporation of intrinsic checkpoint blockade enhances functionality of multigenic autologous UltraCAR-T® cells manufactured using non-viral gene delivery and rapid manufacturing process [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2821.
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Laidig F, Feike T, Klocke B, Macholdt J, Miedaner T, Rentel D, Piepho HP. Long-term breeding progress of yield, yield-related, and disease resistance traits in five cereal crops of German variety trials. Theor Appl Genet 2021; 134:3805-3827. [PMID: 34652455 PMCID: PMC8580907 DOI: 10.1007/s00122-021-03929-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Considerable breeding progress in cereal and disease resistances, but not in stem stability was found. Ageing effects decreased yield and increased disease susceptibility indicating that new varieties are constantly needed. Plant breeding and improved crop management generated considerable progress in cereal performance over the last decades. Climate change, as well as the political and social demand for more environmentally friendly production, require ongoing breeding progress. This study quantified long-term trends for breeding progress and ageing effects of yield, yield-related traits, and disease resistance traits from German variety trials for five cereal crops with a broad spectrum of genotypes. The varieties were grown over a wide range of environmental conditions during 1988-2019 under two intensity levels, without (I1) and with (I2) fungicides and growth regulators. Breeding progress regarding yield increase was the highest in winter barley followed by winter rye hybrid and the lowest in winter rye population varieties. Yield gaps between I2 and I1 widened for barleys, while they shrank for the other crops. A notable decrease in stem stability became apparent in I1 in most crops, while for diseases generally a decrasing susceptibility was found, especially for mildew, brown rust, scald, and dwarf leaf rust. The reduction in disease susceptibility in I2 (treated) was considerably higher than in I1. Our results revealed that yield performance and disease resistance of varieties were subject to considerable ageing effects, reducing yield and increasing disease susceptibility. Nevertheless, we quantified notable achievements in breeding progress for most disease resistances. This study indicated an urgent and continues need for new improved varieties, not only to combat ageing effects and generate higher yield potential, but also to offset future reduction in plant protection intensity.
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Affiliation(s)
- F Laidig
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany.
| | - T Feike
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Strategies and Technology Assessment, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - B Klocke
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Strategies and Technology Assessment, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - J Macholdt
- Institute of Plant Breeding I and Agronomy, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392, Giessen, Germany
- Department of Plant and Environmental Sciences, Section of Environmental Chemistry and Physics, University of Copenhagen, 1871, Frederiksberg, Copenhagen, Denmark
| | - T Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany
| | - D Rentel
- Bundessortenamt, Osterfelddamm 60, 30627, Hannover, Germany
| | - H P Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
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Laidig F, Feike T, Hadasch S, Rentel D, Klocke B, Miedaner T, Piepho HP. Breeding progress of disease resistance and impact of disease severity under natural infections in winter wheat variety trials. Theor Appl Genet 2021; 134:1281-1302. [PMID: 33713338 PMCID: PMC8081715 DOI: 10.1007/s00122-020-03728-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/11/2020] [Indexed: 05/20/2023]
Abstract
Breeding progress of resistance to fungal wheat diseases and impact of disease severity on yield reduction in long-term variety trials under natural infection were estimated by mixed linear regression models. This study aimed at quantifying breeding progress achieved in resistance breeding towards varieties with higher yield and lower susceptibility for 6 major diseases, as well as estimating decreasing yields and increasing disease susceptibility of varieties due to ageing effects during the period 1983-2019. A further aim was the prediction of disease-related yield reductions during 2005-2019 by mixed linear regression models using disease severity scores as covariates. For yield and all diseases, overall progress of the fully treated intensity (I2) was considerably higher than for the intensity without fungicides and growth regulators (I1). The disease severity level was considerably reduced during the study period for mildew (MLD), tan spot (DTR) and Septoria nodorum blotch (ear) (SNB) and to a lesser extent for brown (leaf) rust (BNR) and Septoria tritici blotch (STB), however, not for yellow/stripe rust (YLR). Ageing effects increased susceptibility of varieties strongly for BNR and MLD, but were comparatively weak for SNB and DTR. Considerable yield reductions under high disease severity were predicted for STB (-6.6%), BNR (-6.5%) and yellow rust (YLR, -5.8%), but lower reductions for the other diseases. The reduction for resistant vs. highly susceptible varieties under high severity conditions was about halved for BNR and YLR, providing evidence of resistance breeding progress. The empirical evidence on the functional relations between disease severity, variety susceptibility and yield reductions based on a large-scale multiple-disease field trial data set in German winter wheat is an important contribution to the ongoing discussion on fungicide use and its environmental impact.
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Affiliation(s)
- F Laidig
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany.
| | - T Feike
- Institute for Strategies and Technology Assessment, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - S Hadasch
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
| | - D Rentel
- Bundessortenamt, Osterfelddamm 60, 30627, Hannover, Germany
| | - B Klocke
- Institute for Strategies and Technology Assessment, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - T Miedaner
- University of Hohenheim, State Plant Breeding Institute, Fruwirthstrasse 21, 70599, Stuttgart, Germany
| | - H P Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
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Holvoet P, Klocke B, Vanhaverbeke M, Menten R, Sinnaeve P, Raitoharju E, Lehtimäki T, Oksala N, Zinser C, Janssens S, Sipido K, Lyytikainen LP, Cagnin S. RNA-sequencing reveals that STRN, ZNF484 and WNK1 add to the value of mitochondrial MT-COI and COX10 as markers of unstable coronary artery disease. PLoS One 2019; 14:e0225621. [PMID: 31821324 PMCID: PMC6903720 DOI: 10.1371/journal.pone.0225621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/15/2019] [Accepted: 11/09/2019] [Indexed: 12/23/2022] Open
Abstract
Markers in monocytes, precursors of macrophages, which are related to CAD, are largely unknown. Therefore, we aimed to identify genes in monocytes predictive of a new ischemic event in patients with CAD and/or discriminate between stable CAD and acute coronary syndrome. We included 66 patients with stable CAD, of which 24 developed a new ischemic event, and 19 patients with ACS. Circulating CD14+ monocytes were isolated with magnetic beads. RNA sequencing analysis in monocytes of patients with (n = 13) versus without (n = 11) ischemic event at follow-up and in patients with ACS (n = 12) was validated with qPCR (n = 85). MT-COI, STRN and COX10 predicted new ischemic events in CAD patients (power for separation at 1% error rate of 0.97, 0.90 and 0.77 respectively). Low MT-COI and high STRN were also related to shorter time between blood sampling and event. COX10 and ZNF484 together with MT-COI, STRN and WNK1 separated ACS completely from stable CAD patients. RNA expressions in monocytes of MT-COI, COX10, STRN, WNK1 and ZNF484 were independent of cholesterol lowering and antiplatelet treatment. They were independent of troponin T, a marker of myocardial injury. But, COX10 and ZNF484 in human plaques correlated to plaque markers of M1 macrophage polarization, reflecting vascular injury. Expression of MT-COI, COX10, STRN and WNK1, but not that of ZNF484, PBMCs paired with that in monocytes. The prospective study of relation of MT-COI, COX10, STRN, WNK1 and ZNF484 with unstable CAD is warranted.
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Affiliation(s)
- Paul Holvoet
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
- * E-mail:
| | | | | | - Roxane Menten
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Peter Sinnaeve
- Department of Clinical Cardiology, UZ Leuven, Leuven, Belgium
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Life Sciences University of Tampere, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Life Sciences University of Tampere, Tampere, Finland
| | - Niku Oksala
- Division of Vascular Surgery, Department of Surgery, Tampere University Hospital, Tampere, Finland
| | | | - Stefan Janssens
- Department of Clinical Cardiology, UZ Leuven, Leuven, Belgium
| | - Karin Sipido
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Leo-Pekka Lyytikainen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Life Sciences University of Tampere, Tampere, Finland
| | - Stefano Cagnin
- Department of Biology, CRIBI Biotechnology Centre, Padova, Italy
- CIR-Myo Myology Centre, University of Padova, Padova, Italy
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De Backer G, Jankowski P, Kotseva K, Mirrakhimov E, Reiner Ž, Rydén L, Tokgözoğlu L, Wood D, De Bacquer D, De Backer G, Jankowski P, Kotseva K, Mirrakhimov E, Reiner Z, Rydén L, Tokgözoğlu L, Wood D, De Bacquer D, Kotseva K, De Backer G, Abreu A, Aguiar C, Badariene J, Bruthans J, Castro Conde A, Cifkova R, Crowley J, Davletov K, Bacquer DD, De Smedt D, De Sutter J, Deckers J, Dilic M, Dolzhenko M, Druais H, Dzerve V, Erglis A, Fras Z, Gaita D, Gotcheva N, Grobbee D, Gyberg V, Hasan Ali H, Heuschmann P, Hoes A, Jankowski P, Lalic N, Lehto S, Lovic D, Maggioni A, Mancas S, Marques-Vidal P, Mellbin L, Miličić D, Mirrakhimov E, Oganov R, Pogosova N, Reiner Ž, Rydén L, Stagmo M, Störk S, Sundvall J, Tokgözoğlu L, Tsioufis K, Vulic D, Wood D, Wood D, Kotseva K, Jennings C, Adamska A, Adamska S, Rydén L, Mellbin L, Tuomilehto J, Schnell O, Druais H, Fiorucci E, Glemot M, Larras F, Missiamenou V, Maggioni A, Taylor C, Ferreira T, Lemaitre K, Bacquer DD, De Backer G, Raman L, Sundvall J, DeSmedt D, De Sutter J, Willems A, De Pauw M, Vervaet P, Bollen J, Dekimpe E, Mommen N, Van Genechten G, Dendale P, Bouvier C, Chenu P, Huyberechts D, Persu A, Dilic M, Begic A, Durak Nalbantic A, Dzubur A, Hadzibegic N, Iglica A, Kapidjic S, Osmanagic Bico A, Resic N, Sabanovic Bajramovic N, Zvizdic F, Vulic D, Kovacevic-Preradovic T, Popovic-Pejicic S, Djekic D, Gnjatic T, Knezevic T, Kovacevic-Preradovic T, Kos L, Popovic-Pejicic S, Stanetic B, Topic G, Gotcheva N, Georgiev B, Terziev A, Vladimirov G, Angelov A, Kanazirev B, Nikolaeva S, Tonkova D, Vetkova M, Milicic D, Reiner Ž, Bosnic A, Dubravcic M, Glavina M, Mance M, Pavasovic S, Samardzic J, Batinic T, Crljenko K, Delic-Brkljacic D, Dula K, Golubic K, Klobucar I, Kordic K, Kos N, Nedic M, Olujic D, Sedinic V, Blazevic T, Pasalic A, Percic M, Sikic J, Bruthans J, Cífková R, Hašplová K, Šulc P, Wohlfahrt P, Mayer O, Cvíčela M, Filipovský J, Gelžinský J, Hronová M, Hasan-Ali H, Bakery S, Mosad E, Hamed H, Ibrahim A, Elsharef M, Kholef E, Shehata A, Youssef M, Elhefny E, Farid H, Moustafa T, Sobieh M, Kabil H, Abdelmordy A, Lehto S, Kiljander E, Kiljander P, Koukkunen H, Mustonen J, Cremer C, Frantz S, Haupt A, Hofmann U, Ludwig K, Melnyk H, Noutsias M, Karmann W, Prondzinsky R, Herdeg C, Hövelborn T, Daaboul A, Geisler T, Keller T, Sauerbrunn D, Walz-Ayed M, Ertl G, Leyh R, Störk S, Heuschmann P, Ehlert T, Klocke B, Krapp J, Ludwig T, Käs J, Starke C, Ungethüm K, Wagner M, Wiedmann S, Tsioufis K, Tolis P, Vogiatzi G, Sanidas E, Tsakalis K, Kanakakis J, Koutsoukis A, Vasileiadis K, Zarifis J, Karvounis C, Crowley J, Gibson I, Houlihan A, Kelly C, O'Donnell M, Bennati M, Cosmi F, Mariottoni B, Morganti M, Cherubini A, Di Lenarda A, Radini D, Ramani F, Francese M, Gulizia M, Pericone D, Davletov K, Aigerim K, Zholdin B, Amirov B, Assembekov B, Chernokurova E, Ibragimova F, Kodasbayev A, Markova A, Mirrakhimov E, Asanbaev A, Toktomamatov U, Tursunbaev M, Zakirov U, Abilova S, Arapova R, Bektasheva E, Esenbekova J, Neronova K, Asanbaev A, Baigaziev K, Toktomamatov U, Zakirov U, Baitova G, Zheenbekov T, Erglis A, Andrejeva T, Bajare I, Kucika G, Labuce A, Putane L, Stabulniece M, Dzerve V, Klavins E, Sime I, Badariene J, Gedvilaite L, Pečiuraite D, Sileikienė V, Skiauteryte E, Solovjova S, Sidabraite R, Briedis K, Ceponiene I, Jurenas M, Kersulis J, Martinkute G, Vaitiekiene A, Vasiljevaite K, Veisaite R, Plisienė J, Šiurkaitė V, Vaičiulis Ž, Jankowski P, Czarnecka D, Kozieł P, Podolec P, Nessler J, Gomuła P, Mirek-Bryniarska E, Bogacki P, Wiśniewski A, Pająk A, Wolfshaut-Wolak R, Bućko J, Kamiński K, Łapińska M, Paniczko M, Raczkowski A, Sawicka E, Stachurska Z, Szpakowicz M, Musiał W, Dobrzycki S, Bychowski J, Kosior D, Krzykwa A, Setny M, Kosior D, Rak A, Gąsior Z, Haberka M, Gąsior Z, Haberka M, Szostak-Janiak K, Finik M, Liszka J, Botelho A, Cachulo M, Sousa J, Pais A, Aguiar C, Durazzo A, Matos D, Gouveia R, Rodrigues G, Strong C, Guerreiro R, Aguiar J, Abreu A, Cruz M, Daniel P, Morais L, Moreira R, Rosa S, Rodrigues I, Selas M, Gaita D, Mancas S, Apostu A, Cosor O, Gaita L, Giurgiu L, Hudrea C, Maximov D, Moldovan B, Mosteoru S, Pleava R, Ionescu M, Parepa I, Pogosova N, Arutyunov A, Ausheva A, Isakova S, Karpova A, Salbieva A, Sokolova O, Vasilevsky A, Pozdnyakov Y, Antropova O, Borisova L, Osipova I, Lovic D, Aleksic M, Crnokrak B, Djokic J, Hinic S, Vukasin T, Zdravkovic M, Lalic N, Jotic A, Lalic K, Lukic L, Milicic T, Macesic M, Stanarcic Gajovic J, Stoiljkovic M, Djordjevic D, Kostic S, Tasic I, Vukovic A, Fras Z, Jug B, Juhant A, Krt A, Kugonjič U, Chipayo Gonzales D, Gómez Barrado J, Kounka Z, Marcos Gómez G, Mogollón Jiménez M, Ortiz Cortés C, Perez Espejo P, Porras Ramos Y, Colman R, Delgado J, Otero E, Pérez A, Fernández-Olmo M, Torres-LLergo J, Vasco C, Barreñada E, Botas J, Campuzano R, González Y, Rodrigo M, de Pablo C, Velasco E, Hernández S, Lozano C, González P, Castro A, Dalmau R, Hernández D, Irazusta F, Vélez A, Vindel C, Gómez-Doblas J, García Ruíz V, Gómez L, Gómez García M, Jiménez-Navarro M, Molina Ramos A, Marzal D, Martínez G, Lavado R, Vidal A, Rydén L, Boström-Nilsson V, Kjellström B, Shahim B, Smetana S, Hansen O, Stensgaard-Nake E, Deckers J, Klijn A, Mangus T, Peters R, Scholte op Reimer W, Snaterse M, Aydoğdu S, Ç Erol, Otürk S, Tulunay Kaya C, Ahmetoğlu Y, Ergene O, Akdeniz B, Çırgamış D, Akkoyun H Kültürsay S, Kayıkçıoğlu M, Çatakoğlu A, Çengel A, Koçak A, Ağırbaşlı M, Açıksarı G, Çekin M, Tokgözoğlu L, Kaya E, Koçyiğit D, Öngen Z, Özmen E, Sansoy V, Kaya A, Oktay V, Temizhan A, Ünal S, İ Yakut, Kalkan A, Bozkurt E, Kasapkara H, Dolzhenko M, Faradzh C, Hrubyak L, Konoplianyk L, Kozhuharyova N, Lobach L, Nesukai V, Nudchenko O, Simagina T, Yakovenko L, Azarenko V, Potabashny V, Bazylevych A, Bazylevych M, Kaminska K, Panchenko L, Shershnyova O, Ovrakh T, Serik S, Kolesnik T, Kosova H, Wood D, Adamska A, Adamska S, Jennings C, Kotseva K, Hoye P Atkin A, Fellowes D, Lindsay S, Atkinson C, Kranilla C, Vinod M, Beerachee Y, Bennett C, Broome M, Bwalya A, Caygill L, Dinning L, Gillespie A, Goodfellow R, Guy J, Idress T, Mills C, Morgan C, Oustance N, Singh N, Yare M, Jagoda J, Bowyer H, Christenssen V, Groves A, Jan A, Riaz A, Gill M, Sewell T, Gorog D, Baker M, De Sousa P, Mazenenga T, Porter J, Haines F, Peachey T, Taaffe J, Wells K, Ripley D, Forward H, McKie H, Pick S, Thomas H, Batin P, Exley D, Rank T, Wright J, Kardos A, Sutherland SB, Wren L, Leeson P, Barker D, Moreby B, Sawyer J, Stirrup J, Brunton M, Brodison A, Craig J, Peters S, Kaprielian R, Bucaj A, Mahay K, Oblak M, Gale C, Pye M, McGill Y, Redfearn H, Fearnley M. Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries. Atherosclerosis 2019; 285:135-146. [DOI: 10.1016/j.atherosclerosis.2019.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/22/2019] [Accepted: 03/19/2019] [Indexed: 12/16/2022]
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Dobi A, Petrovics G, Li H, Tan SH, Stümpel T, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Srivastava S. Abstract 140: LSAMP gene deletion is associated with rapid disease progression in prostate cancer of African American men. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
INTRODUCTION: Disproportionately higher rates of prostate cancer (CaP) incidence and mortality have been reported among African American (AA) men. Although oncogenic TMPRSS2-ERG gene fusion and deletion of the PTEN tumor suppressor gene are established cancer driver gene alterations in CaP, they are known to be more prevalent among men of European ancestry. By utilizing carefully annotated specimens, this study focused on the discovery of recurrent genomic alterations in CaP of AA men in comparison to Caucasian Americans (CA).
METHODS: Genomic DNA from clinically localized primary prostate tumors (Gleason 6 or 7 with primary pattern 3) and matched peripheral blood lymphocytes of seven AA and seven CA patients, were analyzed by paired-end sequencing on Illumina Genome Analyzer IIx to a depth of 30x. Following alignment to reference genome, somatic alterations on tumor DNA that include single nucleotide variants (SNVs), insertion and deletions (Indels), structural variations, copy number variations, and inter- and intra-chromosomal translocations of tumor DNA sequence were identified. To confirm prevalent genomic deletions we performed FISH analysis on a tissue microarray constructed from 42 AA and 59 CA tumor and normal samples of an independent cohort. Frequently deleted loci were further validated by analysis of TCGA CaP SNP array data from 41 AA and 279 CA prostate tumors.
RESULTS: A comparative evaluation of whole genome sequences of AA and CA CaP revealed a prevalent deletion of the LSAMP locus of chromosome 3q13.31 in AA CaP. These observations were confirmed by SNP array and FISH assays in independent cohorts of specimens. AA CaP patients with LSAMP deletion showed rapid disease progression. In contrast to higher frequency of LSAMP deletion, significantly lower frequencies of PTEN and ERG alterations were noted in CaP of AA men. Furthermore, CaP genomes of AA men displayed a higher rate of inter-chromosomal rearrangements than those from CA men.
CONCLUSIONS: We highlight distinct features of AA and CA CaP genomes including common CaP driver genes (TMPRSS2- ERG, PTEN) and define a novel recurrent deletion of the LSAMP locus. This study underscores the need for careful evaluations of cancer genomes in underrepresented populations in the global context with implications for precision medicine strategies.
Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Shyh-Han Tan, Tanja Stümpel, Denise Young, Shilpa Katta, Qiyuan Li, Kai Ying, Bernward Klocke, Lakshmi Ravindranath, Indu Kohaar, Yongmei Chen, Dezső Ribli, Korbinian Grote, Hau Zou, Joseph Cheng, Clifton L. Dalgard, Shimin Zhang, István Csabai, Jacob Kagan, David Takeda, Massimo Loda, Sudhir Srivastava, Matthias Scherf, Martin Seifert, Timo Gaiser, David G. McLeod, Zoltan Szallasi, Reinhard Ebner, Thomas Werner, Isabell A. Sesterhenn, Matthew Freedman, Shiv Srivastava. LSAMP gene deletion is associated with rapid disease progression in prostate cancer of African American men. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 140.
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Affiliation(s)
- Albert Dobi
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Gyorgy Petrovics
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Hua Li
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Shyh-Han Tan
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | | | - Denise Young
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Shilpa Katta
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Qiyuan Li
- 3Medical College, Xiamen University, Xiamen, China
| | - Kai Ying
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | | | - Lakshmi Ravindranath
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Indu Kohaar
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Yongmei Chen
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
| | - Dezső Ribli
- 4Eötvös Loránd University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | - Timo Gaiser
- 10Universitätsmedizin Mannheim, Mannheim, Germany
| | - David G. McLeod
- 11Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD
| | | | | | | | | | | | - Shiv Srivastava
- 1Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Rockville, MD
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Nestor CE, Lentini A, Hägg Nilsson C, Gawel DR, Gustafsson M, Mattson L, Wang H, Rundquist O, Meehan RR, Klocke B, Seifert M, Hauck SM, Laumen H, Zhang H, Benson M. 5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4(+) T Cells. Cell Rep 2016; 16:559-570. [PMID: 27346350 DOI: 10.1016/j.celrep.2016.05.091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/24/2016] [Accepted: 05/22/2016] [Indexed: 12/17/2022] Open
Abstract
5-methylcytosine (5mC) is converted to 5-hydroxymethylcytosine (5hmC) by the TET family of enzymes as part of a recently discovered active DNA de-methylation pathway. 5hmC plays important roles in regulation of gene expression and differentiation and has been implicated in T cell malignancies and autoimmunity. Here, we report early and widespread 5mC/5hmC remodeling during human CD4(+) T cell differentiation ex vivo at genes and cell-specific enhancers with known T cell function. We observe similar DNA de-methylation in CD4(+) memory T cells in vivo, indicating that early remodeling events persist long term in differentiated cells. Underscoring their important function, 5hmC loci were highly enriched for genetic variants associated with T cell diseases and T-cell-specific chromosomal interactions. Extensive functional validation of 22 risk variants revealed potentially pathogenic mechanisms in diabetes and multiple sclerosis. Our results support 5hmC-mediated DNA de-methylation as a key component of CD4(+) T cell biology in humans, with important implications for gene regulation and lineage commitment.
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Affiliation(s)
- Colm E Nestor
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden.
| | - Antonio Lentini
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Cathrine Hägg Nilsson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Danuta R Gawel
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Lina Mattson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Hui Wang
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Olof Rundquist
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | | | | | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
| | - Helmut Laumen
- Else Kröner-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, MRI and ZIEL, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes at the Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Huan Zhang
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Mikael Benson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden.
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Tan SH, Petrovics G, Li H, Stümpel T, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S. MP66-05 A NOVEL DELETION OF THE
LSAMP
GENE LOCUS ASSOCIATES WITH RAPID PROGRESSION OF PROSTATE CANCER AMONG AFRICAN AMERICAN MEN. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.1279] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gratwicke B, Ross H, Batista A, Chaves G, Crawford AJ, Elizondo L, Estrada A, Evans M, Garelle D, Guerrel J, Hertz A, Hughey M, Jaramillo CA, Klocke B, Mandica M, Medina D, Richards‐Zawacki CL, Ryan MJ, Sosa‐Bartuano A, Voyles J, Walker B, Woodhams DC, Ibáñez R. Evaluating the probability of avoiding disease‐related extinctions of Panamanian amphibians through captive breeding programs. Anim Conserv 2016. [DOI: 10.1111/acv.12249] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- B. Gratwicke
- Center for Species Survival Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
| | - H. Ross
- Panama Amphibian Rescue and Conservation Project El Valle Amphibian Conservation Center Smithsonian Tropical Research Institute Panama Republic of Panama
| | - A. Batista
- Senckenberg Forschungsinstitut und Naturmuseum Frankfurt Frankfurt Germany
| | - G. Chaves
- Escuela de Biología Universidad de Costa Rica San José Costa Rica
| | - A. J. Crawford
- Department of Biological Sciences Universidad de los Andes Bogotá Colombia
- Smithsonian Tropical Research Institute Panama Republic of Panama
- Círculo Herpetológico de Panamá Panama Republic of Panama
| | - L. Elizondo
- Programa de Maestría en Ciencias Biológicas Universidad de Panamá Panama Republic of Panama
| | - A. Estrada
- Department of Biological Sciences Virginia Tech Blacksburg VA USA
| | - M. Evans
- Reptile Discovery Center Smithsonian's National Zoological Park Washington DC USA
| | - D. Garelle
- Cheyenne Mountain Zoo Colorado Springs CO USA
| | - J. Guerrel
- Panama Amphibian Rescue and Conservation Project Smithsonian Tropical Research Institute Panama Republic of Panama
| | - A. Hertz
- Senckenberg Forschungsinstitut und Naturmuseum Frankfurt Frankfurt Germany
- Institute for Ecology, Evolution and Diversity Biologicum Goethe‐University Frankfurt Germany
| | - M. Hughey
- Department of Biological Sciences Virginia Tech Blacksburg VA USA
| | - C. A. Jaramillo
- Smithsonian Tropical Research Institute Panama Republic of Panama
- Círculo Herpetológico de Panamá Panama Republic of Panama
- Departamento de Histología y Neuroanatomía Humana Facultad de Medicina Universidad de Panamá Panama Republic of Panama
- Biodiversity Consultant Group Panama Republic of Panama
| | - B. Klocke
- Department of Biology George Mason University Fairfax VA USA
| | - M. Mandica
- Department of Research and Conservation Atlanta Botanical Garden Atlanta GA USA
| | - D. Medina
- Department of Biological Sciences Virginia Tech Blacksburg VA USA
| | - C. L. Richards‐Zawacki
- Smithsonian Tropical Research Institute Panama Republic of Panama
- Department of Ecology and Evolutionary Biology Tulane University New Orleans LA USA
| | - M. J. Ryan
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
| | | | | | - B. Walker
- Biodiversity Consultant Group Panama Republic of Panama
| | - D. C. Woodhams
- Smithsonian Tropical Research Institute Panama Republic of Panama
- Department of Biology University of Massachusetts Boston Boston MA USA
| | - R. Ibáñez
- Círculo Herpetológico de Panamá Panama Republic of Panama
- Panama Amphibian Rescue and Conservation Project Smithsonian Tropical Research Institute Panama Republic of Panama
- Departamento de Zoología Universidad de Panamá Panama Republic of Panama
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Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. EBioMedicine 2015; 2:1957-64. [PMID: 26844274 PMCID: PMC4703707 DOI: 10.1016/j.ebiom.2015.10.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 09/11/2015] [Revised: 10/22/2015] [Accepted: 10/29/2015] [Indexed: 02/03/2023] Open
Abstract
Evaluation of cancer genomes in global context is of great interest in light of changing ethnic distribution of the world population. We focused our study on men of African ancestry because of their disproportionately higher rate of prostate cancer (CaP) incidence and mortality. We present a systematic whole genome analyses, revealing alterations that differentiate African American (AA) and Caucasian American (CA) CaP genomes. We discovered a recurrent deletion on chromosome 3q13.31 centering on the LSAMP locus that was prevalent in tumors from AA men (cumulative analyses of 435 patients: whole genome sequence, 14; FISH evaluations, 101; and SNP array, 320 patients). Notably, carriers of this deletion experienced more rapid disease progression. In contrast, PTEN and ERG common driver alterations in CaP were significantly lower in AA prostate tumors compared to prostate tumors from CA. Moreover, the frequency of inter-chromosomal rearrangements was significantly higher in AA than CA tumors. These findings reveal differentially distributed somatic mutations in CaP across ancestral groups, which have implications for precision medicine strategies.
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Affiliation(s)
- Gyorgy Petrovics
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Hua Li
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | | | - Shyh-Han Tan
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Denise Young
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Shilpa Katta
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kai Ying
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | | | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Indu Kohaar
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Yongmei Chen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Dezső Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest H-1117, Hungary; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark
| | | | - Hua Zou
- CytoTest Inc., Rockville, MD 20850, USA
| | | | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Shimin Zhang
- Genitourinary Pathology, Joint Pathology Center, Silver Spring, MD 20910, USA
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest H-1117, Hungary; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Takeda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Massimo Loda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA
| | | | | | - Timo Gaiser
- Pathologisches Institut, Universitätsmedizin Mannheim, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim D-68167, Germany
| | - David G McLeod
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; Urology Service, Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark; Children's Hospital Informatics Program at the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 20115, USA; MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, 2nd Department of Pathology, Semmelweis University, Budapest H-1091, Hungary
| | | | - Thomas Werner
- Genomatix Software GmbH, MünchenE D-80335, Germany; Internal Medicine, Nephrology Division and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Matthew Freedman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Albert Dobi
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Shiv Srivastava
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
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Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K, Wahl S, Hoffmann C, Qian K, Rönn T, Riess H, Müller-Nurasyid M, Bretschneider N, Schroeder T, Skurk T, Horsthemke B, Spieler D, Klingenspor M, Seifert M, Kern MJ, Mejhert N, Dahlman I, Hansson O, Hauck SM, Blüher M, Arner P, Groop L, Illig T, Suhre K, Hsu YH, Mellgren G, Hauner H, Laumen H. Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms. Cell 2014; 156:343-58. [PMID: 24439387 DOI: 10.1016/j.cell.2013.10.058] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 09/05/2013] [Accepted: 10/30/2013] [Indexed: 10/25/2022]
Abstract
Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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Affiliation(s)
- Melina Claussnitzer
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA.
| | - Simon N Dankel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Harald Grallert
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Viktoria Glunk
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Tea Berulava
- Institut für Humangenetik, Universitätsklinikum Essen, Universität-Duisburg-Essen, 45147 Essen, Germany
| | - Heekyoung Lee
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Nikolay Oskolkov
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Joao Fadista
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Kerstin Ehlers
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Simone Wahl
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christoph Hoffmann
- Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Chair of Molecular Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany
| | - Kun Qian
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Tina Rönn
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Helene Riess
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, 89081 Ulm, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany; Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | | | - Timm Schroeder
- Research Unit Stem Cell Dynamics, Helmholtz Center Munich-German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland
| | - Thomas Skurk
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität-Duisburg-Essen, 45147 Essen, Germany
| | | | - Derek Spieler
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, German Research Center for Environmental Health, Germany; Department of Neurology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Martin Klingenspor
- Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Chair of Molecular Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany
| | | | - Michael J Kern
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Niklas Mejhert
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Ola Hansson
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Peter Arner
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Leif Groop
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Hanover Unified Biobank, Hanover Medical School, 30625 Hanover, Germany
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA; Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115, USA
| | - Gunnar Mellgren
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
| | - Hans Hauner
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Helmut Laumen
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany.
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Yadav SP, Hao H, Yang HJ, Kautzmann MAI, Brooks M, Nellissery J, Klocke B, Seifert M, Swaroop A. The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Hum Mol Genet 2013; 23:2132-44. [PMID: 24301678 DOI: 10.1093/hmg/ddt609] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phototransduction machinery in vertebrate photoreceptors is contained within the membrane discs of outer segments. Daily renewal of 10% of photoreceptor outer segments requires stringent control of gene expression. Rhodopsin constitutes over 90% of the protein in rod discs, and its altered expression or transport is associated with photoreceptor dysfunction and/or death. Two cis-regulatory sequences have been identified upstream of the rhodopsin transcription start site. While the proximal promoter binds to specific transcription factors, including NRL and CRX, the rhodopsin enhancer region (RER) reportedly contributes to precise and high-level expression of rhodopsin in vivo. Here, we report the identification of RER-bound proteins by mass spectrometry. We validate the binding of NonO (p54(nrb)), a protein implicated in coupling transcription to splicing, and three NonO-interacting proteins-hnRNP M, Ywhaz and Ppp1ca. NonO and its interactors can activate rhodopsin promoter in HEK293 cells and function synergistically with NRL and CRX. DNA-binding domain of NonO is critical for rhodopsin promoter activation. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analysis demonstrates high occupancy of NonO at rhodopsin and a subset of phototransduction genes. Furthermore, shRNA knockdown of NonO in mouse retina leads to loss of rhodopsin expression and rod cell death, which can be partially rescued by a C-terminal NonO construct. RNA-seq analysis of the NonO shRNA-treated retina revealed splicing defects and altered expression of genes, specifically those associated with phototransduction. Our studies identify an important contribution of NonO and its interacting modulator proteins in enhancing rod-specific gene expression and controlling rod homeostasis.
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Affiliation(s)
- Sharda P Yadav
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Supper J, Gugenmus C, Wollnik J, Drueke T, Scherf M, Hahn A, Grote K, Bretschneider N, Klocke B, Zinser C, Cartharius K, Seifert M. Detecting and visualizing gene fusions. Methods 2012; 59:S24-8. [PMID: 23036331 DOI: 10.1016/j.ymeth.2012.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In recent years, gene fusions have gained significant recognition as biomarkers. They can assist treatment decisions, are seldom found in normal tissue and are detectable through Next-generation sequencing (NGS) of the transcriptome (RNA-seq). To transform the data provided by the sequencer into robust gene fusion detection several analysis steps are needed. Usually the first step is to map the sequenced transcript fragments (RNA-seq) to a reference genome. One standard application of this approach is to estimate expression and detect variants within known genes, e.g. SNPs and indels. In case of gene fusions, however, completely novel gene structures have to be detected. Here, we describe the detection of such gene fusion events based on our comprehensive transcript annotation (ElDorado). To demonstrate the utility of our approach, we extract gene fusion candidates from eight breast cancer cell lines, which we compare to experimentally verified gene fusions. We discuss several gene fusion events, like BCAS3-BCAS4 that was only detected in the breast cancer cell line MCF7. As supporting evidence we show that gene fusions occur more frequently in copy number enriched regions (CNV analysis). In addition, we present the Transcriptome Viewer (TViewer) a tool that allows to interactively visualize gene fusions. Finally, we support detected gene fusions through literature mining based annotations and network analyses. In conclusion, we present a platform that allows detecting gene fusions and supporting them through literature knowledge as well as rich visualization capabilities. This enables scientists to better understand molecular processes, biological functions and disease associations, which will ultimately lead to better biomedical knowledge for the development of biomarkers for diagnostics and therapies.
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Affiliation(s)
- Jochen Supper
- Genomatix Software GmbH, Bayerstr. 85a, 80335 München, Germany.
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Vikström Bergander L, Cai W, Klocke B, Seifert M, Pongratz I. Tryptamine serves as a proligand of the AhR transcriptional pathway whose activation is dependent of monoamine oxidases. Mol Endocrinol 2012; 26:1542-51. [PMID: 22865928 DOI: 10.1210/me.2011-1351] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The function of the aryl hydrocarbon receptor (AhR) in mediating the biological effect to environmental pollutants is well established. However, accumulated evidence indicates a wide range of physiological and pathological functions mediated by the AhR, suggesting the existence of endogenous AhR ligand(s). The nature of an AhR ligand remain elusive; however, it is known that the AhR is activated by several compounds, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin or the tryptophan photoproduct 6-formylindolo[3,2-b]carbazole. In this study, we show that physiological concentrations of tryptamine (TA) lead to induction of cytochrome P4501A1 transcription through an AhR-dependent mechanism. In addition, we show that activation of the AhR by TA requires a functional monoamino oxidase system, suggesting that TA acts as an AhR proligand possibly by converting to a high-affinity AhR ligand. Taken together, we show a possible mechanism, through which AhR signaling is activated by endogenous conversion of TA involving monoamine oxidases.
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Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. PLoS Genet 2012; 8:e1002649. [PMID: 22511886 PMCID: PMC3325202 DOI: 10.1371/journal.pgen.1002649] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [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: 11/16/2011] [Accepted: 02/23/2012] [Indexed: 11/18/2022] Open
Abstract
A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP-Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP-Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s) for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis.
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Affiliation(s)
- Hong Hao
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas S. Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Kory R. Johnson
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kairong Cui
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Norimoto Gotoh
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chongzhi Zang
- Department of Physics, The George Washington University, Washington, D.C., United States of America
| | - Janina Gregorski
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Linn Gieser
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, D.C., United States of America
| | - Yang Fann
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Abstract
LitInspector is a literature search tool providing gene and signal transduction pathway mining within NCBI's PubMed database. The automatic gene recognition and color coding increases the readability of abstracts and significantly speeds up literature research. A main challenge in gene recognition is the resolution of homonyms and rejection of identical abbreviations used in a ‘non-gene’ context. LitInspector uses automatically generated and manually refined filtering lists for this purpose. The quality of the LitInspector results was assessed with a published dataset of 181 PubMed sentences. LitInspector achieved a precision of 96.8%, a recall of 86.6% and an F-measure of 91.4%. To further demonstrate the homonym resolution qualities, LitInspector was compared to three other literature search tools using some challenging examples. The homonym MIZ-1 (gene IDs 7709 and 9063) was correctly resolved in 87% of the abstracts by LitInspector, whereas the other tools achieved recognition rates between 35% and 67%. The LitInspector signal transduction pathway mining is based on a manually curated database of pathway names (e.g. wingless type), pathway components (e.g. WNT1, FZD1), and general pathway keywords (e.g. signaling cascade). The performance was checked for 10 randomly selected genes. Eighty-two per cent of the 38 predicted pathway associations were correct. LitInspector is freely available at http://www.litinspector.org/.
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Mutch DM, Klocke B, Morrison P, Murray CA, Henderson CJ, Seifert M, Williamson G. The Disruption of Hepatic Cytochrome P450 Reductase Alters Mouse Lipid Metabolism. J Proteome Res 2007; 6:3976-84. [PMID: 17722906 DOI: 10.1021/pr0700448] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To elucidate the role of hepatic cytochrome P450 oxidoreductase (POR) in lipid metabolism, we characterized perturbations in lipid homeostasis in a mouse model deficient in liver POR. Using an integrative approach in which transcriptomics, lipidomics, and various bioinformatic algorithms were employed, a disruption in liver lipid mobilization, oxidation, and electron transport functions were identified. Analyzing the promoters of genes in these biological processes identified common binding motifs for nuclear receptors sensitive to lipid status, while Srebp-1c binding sites were only identified in genes involved in lipid metabolism. POR-null mice had drastic increases in hepatic lipid content (diacylglycerols, triacylglycerols, phosphatidylcholine, and cholesterol esters) and a specific enrichment in n-7 and n-9 monounsaturated fatty acids (FAs). It was found that while transporters involved in peroxisomal FA oxidation were induced, mitochondrial oxidation appeared to be more tightly controlled, supporting the increase in monounsaturated FAs. Genes coding for hepatic transporters were differentially expressed, where lipid uptake was induced and efflux repressed, indicating that in the absence of hepatic POR the liver serves as a lipid reservoir. Furthermore, while significant changes in intestinal gene expression were found in POR-deficient mice, only minor changes to plasma and intestinal lipid content were observed. Thus, while liver POR plays an important role regulating gene expression and lipid metabolism locally, the hepatic deficiency of this enzyme reverberates throughout the biological system and produces a coordinated response to the low levels of circulating cholesterol and bile.
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Affiliation(s)
- David M Mutch
- Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland.
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Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005; 21:2933-42. [PMID: 15860560 DOI: 10.1093/bioinformatics/bti473] [Citation(s) in RCA: 1561] [Impact Index Per Article: 82.2] [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: 01/04/2023] Open
Abstract
MOTIVATION Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. RESULTS We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
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Affiliation(s)
- K Cartharius
- Genomatix Software GmbH Landsberger Strasse. 6, 80339 München, Germany.
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21
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Roux SR, Hackauf B, Linz A, Ruge B, Klocke B, Wehling P. Leaf-rust resistance in rye (Secale cereale L.). 2. Genetic analysis and mapping of resistance genes Pr3, Pr4, and Pr5. Theor Appl Genet 2004; 110:192-201. [PMID: 15378246 DOI: 10.1007/s00122-004-1807-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 08/24/2004] [Indexed: 05/02/2023]
Abstract
Three dominant resistance genes, Pr3, Pr4, and Pr5, were identified by genetic analysis of resistance to leaf rust in rye (Puccinia recondita f. sp. secalis). Each of the three genes confers resistance to a broad scale of single-pustule isolates (SPIs), but differences could be observed for specific Pr gene/SPI combinations. Resistance conferred by the three genes was effective in both detached-leaf tests carried out on seedlings and in field tests of adult plants. Molecular marker analysis mapped Pr3 to the centromeric region of rye chromosome arm 1RS, whereas Pr4 and Pr5 were assigned to the centromeric region of 1RL. Chromosomal localization and reaction patterns to specific SPIs provide evidence that the three Pr genes represent distinct and novel leaf-rust resistance genes in rye. The contributions of these genes to resistance breeding in rye and wheat are discussed.
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Affiliation(s)
- S R Roux
- Institute of Agricultural Crops, Federal Centre for Breeding Research on Cultivated Plants, Rudolf-Schick-Platz 3a, 18190 Gross Lüsewitz, Germany.
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22
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Tasheva ES, Klocke B, Conrad GW. Analysis of transcriptional regulation of the small leucine rich proteoglycans. Mol Vis 2004; 10:758-72. [PMID: 15496828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
PURPOSE Small leucine rich proteoglycans (SLRPs) constitute a family of secreted proteoglycans that are important for collagen fibrillogenesis, cellular growth, differentiation, and migration. Ten of the 13 known members of the SLRP gene family are arranged in tandem clusters on human chromosomes 1, 9, and 12. Their syntenic equivalents are on mouse chromosomes 1, 13, and 10, and rat chromosomes 13, 17, and 7. The purpose of this study was to determine whether there is evidence for control elements, which could regulate the expression of these clusters coordinately. METHODS Promoters were identified using a comparative genomics approach and Genomatix software tools. For each gene a set of human, mouse, and rat orthologous promoters was extracted from genomic sequences. Transcription factor (TF) binding site analysis combined with a literature search was performed using MatInspector and Genomatix' BiblioSphere. Inspection for the presence of interspecies conserved scaffold/matrix attachment regions (S/MARs) was performed using ElDorado annotation lists. DNAseI hypersensitivity assay, chromatin immunoprecipitation (ChIP), and transient transfection experiments were used to validate the results from bioinformatics analysis. RESULTS Transcription factor binding site analysis combined with a literature search revealed co-citations between several SLRPs and TFs Runx2 and IRF1, indicating that these TFs have potential roles in transcriptional regulation of the SLRP family members. We therefore inspected all of the SLRP promoter sets for matches to IRF factors and Runx factors. Positionally conserved binding sites for the Runt domain TFs were detected in the proximal promoters of chondroadherin (CHAD) and osteomodulin (OMD) genes. Two significant models (two or more transcription factor binding sites arranged in a defined order and orientation within a defined distance range) were derived from these initial promoter sets, the HOX-Runx (homeodomain-Runt domain), and the ETS-FKHD-STAT (erythroblast transformation specific-forkhead-signal transducers and activators of transcription) models. These models were used to scan the genomic sequences of all 13 SLRP genes. The HOX-Runx model was found within the proximal promoter, exon 1, or intron 1 sequences of 11 of the 13 SLRP genes. The ETS-FKHD-STAT model was found in only 5 of these genes. Transient transfections of MG-63 cells and bovine corneal keratocytes with Runx2 isoforms confirmed the relevance of these TFs to expression of several SLRP genes. Distribution of the HOX-Runx and ETS-FKHD-STAT models within 200 kb of genomic sequence on human chromosome 9 and 500 kb sequence on chromosome 12 also were analyzed. Two regions with 3 HOX-Runx matches within a 1,000 bp window were identified on human chromosome 9; one located between OMD and osteoglycin (OGN)/mimecan genes, and the second located upstream of the putative extracellular matrix protein 2 (ECM2) promoter. The intergenic region between OMD and mimecan was shown to coincide with different patterns of DNAse I hypersensitivity sites in MG-63 and U937 cells. ChiP analysis revealed that this region binds Runx2 in U937 cells (mimecan transcript note detectable), but binds Pitx3 in MG-63 cells (expressing high level of mimecan), thereby demonstrating its functional association with mimecan expression. Upon comparing the predictions of S/MARs on the relevant chromosomal context of human chromosomes 9 and 12 and their rodent equivalents, no convincing evidence was found that the tandemly arranged genes build a chromosomal loop. CONCLUSIONS Twelve of 13 known SLRP genes have at least one HOX-Runx module match in their promoter, exon 1, intron 1, or intergenic region. Although these genes are located in different clusters on different chromosomes, the common HOX-Runx module could be the basis for co-regulated expression.
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Affiliation(s)
- Elena S Tasheva
- Kansas State University, Division of Biology, Manhattan, KS 66506-4901, USA.
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Wehling P, Linz A, Hackauf B, Roux SR, Ruge B, Klocke B. Leaf-rust resistance in rye (Secale cereale L.). 1. Genetic analysis and mapping of resistance genes Pr1 and Pr2. Theor Appl Genet 2003; 107:432-438. [PMID: 12721636 DOI: 10.1007/s00122-003-1263-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2003] [Accepted: 02/12/2003] [Indexed: 05/24/2023]
Abstract
Genetic analysis of resistance to leaf rust in rye (Puccinia recondita f. sp. secalis) led to the identification of two dominant resistance genes, Pr1 and Pr2. Both genes proved to be effective against a local leaf-rust population as well as a subset of single-pustule isolates (SPIs) the latter of which comprised SPIs with very high virulence complexity. Resistance conferred by Pr1 and Pr2 was expressed in detached-leaf tests of seedlings as well as in field tests of adult plants. Molecular marker analysis allowed us to map Pr1 in the proximal part of rye chromosome 6RL, whereas Pr2 was assigned to the distal part of chromosome 7RL. These results are discussed in view of homoeology relationships among Triticeae. A proposal is submitted for the designation of resistance genes to rye leaf rust which would avoid interference with existing gene-symboling in respect to wheat leaf-rust resistances introgressed from rye into wheat or triticale.
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Affiliation(s)
- P Wehling
- Institute of Agricultural Crops, Federal Centre for Breeding Research on Cultivated Plants (BAZ), Rudolf-Schick-Platz 3a, 18190 Gross Lüsewitz, Germany.
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24
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Rinkenberger JL, Horning S, Klocke B, Roth K, Korsmeyer SJ. Mcl-1 deficiency results in peri-implantation embryonic lethality. Genes Dev 2000; 14:23-7. [PMID: 10640272 PMCID: PMC316347] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We disrupted the Mcl-1 locus in murine ES cells to determine the developmental roles of this Bcl-2 family member. Deletion of Mcl-1 resulted in peri-implantation embryonic lethality. Mcl-1(-/-) embryos do not implant in utero, but could be recovered at E3.5-4.0. Null blastocysts failed to hatch or attach in vitro, indicating a trophectoderm defect, although the inner cell mass could grow in culture. Of note, Mcl-1(-/-) blastocysts showed no evidence of increased apoptosis, but exhibited a delay in maturation beyond the precompaction stage. This model indicates that Mcl-1 is essential for preimplantation development and implantation, and suggests that it has a function beyond regulating apoptosis.
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Affiliation(s)
- J L Rinkenberger
- Departments of Medicine and Pathology, Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri 63110 USA
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Yin XM, Wang K, Gross A, Zhao Y, Zinkel S, Klocke B, Roth KA, Korsmeyer SJ. Bid-deficient mice are resistant to Fas-induced hepatocellular apoptosis. Nature 1999; 400:886-91. [PMID: 10476969 DOI: 10.1038/23730] [Citation(s) in RCA: 770] [Impact Index Per Article: 30.8] [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: 12/15/2022]
Abstract
The protein Bid is a participant in the pathway that leads to cell death (apoptosis), mediating the release of cytochrome c from mitochondria in response to signals from 'death' receptors known as TNFR1/Fas on the cell surface. It is a member of the proapoptotic Bcd-2 family and is activated as a result of its cleavage by caspase 8, one of a family of proteolytic cell-death proteins. To investigate the role of Bid in vivo, we have generated mice deficient for Bid. We find that when these mice are injected with an antibody directed against Fas, they nearly all survive, whereas wild-type mice die from hepatocellular apoptosis and haemorrhagic necrosis. About half of the Bid-deficient animals had no apparent liver injury and showed no evidence of activation of the effector caspases 3 and 7, although the initiator caspase 8 had been activated. Other Bid-deficient mice survived with only moderate damage: all three caspases (8 and 37) were activated but their cell nuclei were intact and no mitochondrial cytochrome c was released. We also investigated the effects of Bid deficiency in cultured cells treated with anti-Fas antibody (hepatocytes and thymocytes) or with TNFalpha. (fibroblasts). In these Bid-/- cells, mitochondrial dysfunction was delayed, cytochrome c was not released, effector caspase activity was reduced and the cleavage of apoptosis substrates was altered. This loss-of-function model indicates that Bid is a critical substrate in vivo for signalling by death-receptor agonists, which mediates a mitochondrial amplification loop that is essential for the apoptosis of selected cells.
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Affiliation(s)
- X M Yin
- Department of Pathology, Washington University School of Medicine, Howard Hughes Medical Institute, St Louis, Missouri 63110, USA
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Abstract
Zn finger proteins (ZFPs) of the C2/H2 type in Xenopus laevis are encoded by a multigene family comprising several hundred members. Based upon conserved sequence features outside the Zn finger region, ZFPs can be subdivided into distinct subfamilies. Two of such subfamilies are characterized by conserved, N-terminal amino acid sequences termed the FAX and the FAR Domain. Here we present data suggesting that the zinc finger proteins of the FAR-ZFP subfamily are targets for CK II mediated phosphorylation. Expression of these proteins during oogenesis coincides with CK II activity in unfertilized eggs. Additionally, we have found that XlcOF 7.1, a member of the FAX-ZFP subfamily, is also phosphorylated by CK II. The target sites for in vitro phosphorylation are localized within the conserved N-terminal domains but not within the Zn finger regions. However, amino acid sequence comparison revealed that individual phosphoacceptor sites are not generally conserved among all members of the respective ZFP subfamilies. The relevance of a potential CK II phosphorylation for the regulation of ZFP activity in vivo is discussed.
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Affiliation(s)
- B Klocke
- Abt. Biochemie, Universität Ulm, Germany
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Klocke B, Köster M, Hille S, Bouwmeester T, Böhm S, Pieler T, Knöchel W. The FAR domain defines a new Xenopus laevis zinc finger protein subfamily with specific RNA homopolymer binding activity. Biochim Biophys Acta 1994; 1217:81-9. [PMID: 7506934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The zinc finger motif defines a large superfamily of nucleic acid binding proteins. Conserved amino acid sequence elements associated with structurally variant zinc finger clusters define subfamilies of zinc finger proteins (ZFPs). The FAR domain (Finger Associated Repeats) is a novel type of repeat element found at the amino-terminus in a subfamily of Xenopus laevis ZFPs. Northern blot analyses of three different members of the FAR subfamily (XFO 6, XFO 9-3 and XFG 68) revealed that each of these genes is transcribed during oogenesis, embryogenesis and in all investigated tissues of adult animals thereby indicating a ubiquitous distribution of transcripts. All FAR-ZFPs tested so far have specific RNA homopolymer binding activity; they associate preferentially with poly(U). The FAR repeats possess limited primary sequence homology with a sequence in the nucleolar shuttling protein NO38, within a region that contains a casein kinase II phosphorylation site.
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Affiliation(s)
- B Klocke
- Abteilung Biochemie, Universität Ulm, Germany
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Klocke B, Köster M, Hille S, Bouwmeester T, Böhm S, Pieler T, Knöchel W. The FAR domain defines a new Xenopus laevis zinc finger protein subfamily with specific RNA homopolymer binding activity. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0167-4781(94)90127-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Knöchel S, Lef J, Clement J, Klocke B, Hille S, Köster M, Knöchel W. Activin A induced expression of a fork head related gene in posterior chordamesoderm (notochord) of Xenopus laevis embryos. Mech Dev 1992; 38:157-65. [PMID: 1358174 DOI: 10.1016/0925-4773(92)90007-7] [Citation(s) in RCA: 99] [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: 01/17/2023]
Abstract
A gene family encoding the fork head/HNF-3 domain has been identified in the South African clawed frog, Xenopus laevis. Screening of genomic DNA and gastrula stage derived cDNA libraries with a DNA fragment encoding the Drosophila fork head domain led to the isolation of a number of different clones encoding this motif. While one of the Xenopus fork head sequences, XFD-3, represents the Xenopus counterpart to rat HNF-3 beta, all other sequences encode novel types of fork head related proteins. Here we report on XFD-1, a DNA binding protein which can bind to the HNF-3 alpha target sequence. Analysis of temporal and spatial expression revealed that the gene is activated at blastula stage and that transcripts are localized in a rather thin stripe of cells invaginating the dorsal blastopore lip (organizer) during gastrulation. XFD-1 mRNA is localized within the notochord and, by the end of neurulation, is no longer detectable. In the animal cap assay the gene is activated by incubation with the vegetalizing factor (activin A) but not with bFGF.
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Affiliation(s)
- S Knöchel
- Abteilung Biochemie, Universität Ulm, Germany
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