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Horn H, Morales Y, Samanta P, Saravia F. Water management for Power‐to‐X. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202255222] [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: 11/05/2022]
Affiliation(s)
- H. Horn
- DVGW-Research Center at the Engler-Bunte-Institut Engler-Bunte Ring 9 76131 Karlsruhe Germany
| | - Y. Morales
- DVGW-Research Center at the Engler-Bunte-Institut Engler-Bunte Ring 9 76131 Karlsruhe Germany
| | - P. Samanta
- DVGW-Research Center at the Engler-Bunte-Institut Engler-Bunte Ring 9 76131 Karlsruhe Germany
| | - F. Saravia
- DVGW-Research Center at the Engler-Bunte-Institut Engler-Bunte Ring 9 76131 Karlsruhe Germany
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2
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Gmurek M, Borowska E, Schwartz T, Horn H. Does light-based tertiary treatment prevent the spread of antibiotic resistance genes? Performance, regrowth and future direction. Sci Total Environ 2022; 817:153001. [PMID: 35031375 DOI: 10.1016/j.scitotenv.2022.153001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
The common occurrence of antibiotic-resistance genes (ARGs) originating from pathogenic and facultative pathogenic bacteria pose a high risk to aquatic environments. Low removal of ARGs in conventional wastewater treatment processes and horizontal dissemination of resistance genes between environmental bacteria and human pathogens have made antibiotic resistance evolution a complex global health issue. The phenomenon of regrowth of bacteria after disinfection raised some concerns regarding the long-lasting safety of treated waters. Despite the inactivation of living antibiotic-resistant bacteria (ARB), the possibility of transferring intact and liberated DNA containing ARGs remains. A step in this direction would be to apply new types of disinfection methods addressing this issue in detail, such as light-based advanced oxidation, that potentially enhance the effect of direct light interaction with DNA. This study is devoted to comprehensively and critically review the current state-of-art for light-driven disinfection. The main focus of the article is to provide an insight into the different photochemical disinfection methods currently being studied worldwide with respect to ARGs removal as an alternative to conventional methods. The systematic comparison of UV/chlorination, UV/H2O2, sulfate radical based-AOPs, photocatalytic processes and photoFenton considering their mode of action on molecular level, operational parameters of the processes, and overall efficiency of removal of ARGs is presented. An in-depth discussion of different light-dependent inactivation pathways, influence of DBP and DOM on ARG removal and the potential bacterial regrowth after treatment is presented. Based on presented revision the risk of ARG transfer from reactivated bacteria has been evaluated, leading to a future direction for research addressing the challenges of light-based disinfection technologies.
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Affiliation(s)
- M Gmurek
- Department of Molecular Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, 90-924 Lodz, Poland; Karlsruhe Institute of Technology, Engler-Bunte-Institut, Water Chemistry and Water Technology, 76131 Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute of Functional Interfaces, Microbiology/Molecular Biology Department, Eggenstein-Leopoldshafen, Germany.
| | - E Borowska
- Karlsruhe Institute of Technology, Engler-Bunte-Institut, Water Chemistry and Water Technology, 76131 Karlsruhe, Germany
| | - T Schwartz
- Karlsruhe Institute of Technology, Institute of Functional Interfaces, Microbiology/Molecular Biology Department, Eggenstein-Leopoldshafen, Germany
| | - H Horn
- Karlsruhe Institute of Technology, Engler-Bunte-Institut, Water Chemistry and Water Technology, 76131 Karlsruhe, Germany; DVGW German Technical and Scientific Association for Gas and Water Research Laboratories, Water Chemistry and Water Technology, 76131 Karlsruhe, Germany
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Layer M, Bock K, Ranzinger F, Horn H, Morgenroth E, Derlon N. Particulate substrate retention in plug-flow and fully-mixed conditions during operation of aerobic granular sludge systems. Water Res X 2020; 9:100075. [PMID: 33196033 PMCID: PMC7645637 DOI: 10.1016/j.wroa.2020.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/03/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Particulate substrate (XB) is the major organic substrate fraction in most municipal wastewaters. However, the impact of XB on aerobic granular sludge (AGS) systems is not fully understood. This study evaluated the physical retention of XB in AGS sequencing batch reactor (SBR) during anaerobic plug-flow and then aerobic fully-mixed conditions. The influence of different sludge types and operational variables on the extent and mechanisms of XB retention in AGS SBR were evaluated. XB mass-balancing and magnetic resonance imaging (MRI) were applied. During the anaerobic plug-flow feeding, most XB was retained in the first few cm of the settled sludge bed within the interstitial voids, where XB settled and accumulated ultimately resulting in the formation of a filter-cake. Sedimentation and surface filtration were thus the dominant XB retention mechanisms during plug-flow conditions, indicating that contact and attachment of XB to the biomass was limited. XB retention was variable and influenced by the XB influent concentration, sludge bed composition and upflow feeding velocity (vww). XB retention increased with larger XB influent concentrations and lower vww, which demonstrated the importance of sedimentation on XB retention during plug-flow conditions. Hence, large fractions of influent XB likely re-suspended during aerobic fully-mixed conditions, where XB then preferentially and rapidly attached to the flocs. During fully-mixed conditions, increasing floc fractions, longer mixing times and larger XB concentrations increased XB retention. Elevated XB retention was observed after short mixing times < 60 min when flocs were present, and the contribution of flocs towards XB retention was even more pronounced for short mixing times < 5 min. Overall, our results suggest that flocs occupy an environmental niche that results from the availability of XB during aerobic fully-mixed conditions of AGS SBR. Therefore, a complete wash-out of flocs is not desirable in AGS systems treating municipal wastewater.
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Affiliation(s)
- M. Layer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- ETH Zürich, Institute of Environmental Engineering, 8093, Zürich, Switzerland
| | - K. Bock
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - F. Ranzinger
- Engler-Bunte-Institut, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - H. Horn
- Engler-Bunte-Institut, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - E. Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- ETH Zürich, Institute of Environmental Engineering, 8093, Zürich, Switzerland
| | - N. Derlon
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
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Iyer S, Zhang S, Yucel S, Horn H, Smith SG, Reinhardt F, Hoefsmit E, Assatova B, Casado J, Meinsohn MC, Barrasa MI, Bell GW, Pérez-Villatoro F, Huhtinen K, Hynninen J, Oikkonen J, Galhenage PM, Pathania S, Hammond PT, Neel BG, Farkkila A, Pépin D, Weinberg RA. Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy. Cancer Discov 2020; 11:384-407. [PMID: 33158843 DOI: 10.1158/2159-8290.cd-20-0818] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
Despite advances in immuno-oncology, the relationship between tumor genotypes and response to immunotherapy remains poorly understood, particularly in high-grade serous tubo-ovarian carcinomas (HGSC). We developed a series of mouse models that carry genotypes of human HGSCs and grow in syngeneic immunocompetent hosts to address this gap. We transformed murine-fallopian tube epithelial cells to phenocopy homologous recombination-deficient tumors through a combined loss of Trp53, Brca1, Pten, and Nf1 and overexpression of Myc and Trp53 R172H, which was contrasted with an identical model carrying wild-type Brca1. For homologous recombination-proficient tumors, we constructed genotypes combining loss of Trp53 and overexpression of Ccne1, Akt2, and Trp53 R172H, and driven by KRAS G12V or Brd4 or Smarca4 overexpression. These lines form tumors recapitulating human disease, including genotype-driven responses to treatment, and enabled us to identify follistatin as a driver of resistance to checkpoint inhibitors. These data provide proof of concept that our models can identify new immunotherapy targets in HGSC. SIGNIFICANCE: We engineered a panel of murine fallopian tube epithelial cells bearing mutations typical of HGSC and capable of forming tumors in syngeneic immunocompetent hosts. These models recapitulate tumor microenvironments and drug responses characteristic of human disease. In a Ccne1-overexpressing model, immune-checkpoint resistance was driven by follistatin.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
- Sonia Iyer
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Shuang Zhang
- Laura and Isaac Perlmutter Cancer Center, NYU-Langone Medical Center, New York, New York
| | - Simge Yucel
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Heiko Horn
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Pediatric Surgical Research Laboratories, Massachusetts General Hospital; Department of Surgery, Harvard Medical School, Boston, Massachusetts
| | - Sean G Smith
- Marble Center for Cancer Nanomedicine, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Esmee Hoefsmit
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | | | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marie-Charlotte Meinsohn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital; Department of Surgery, Harvard Medical School, Boston, Massachusetts
| | | | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Fernando Pérez-Villatoro
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pamoda M Galhenage
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, Massachusetts
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, Massachusetts
| | - Paula T Hammond
- Marble Center for Cancer Nanomedicine, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Benjamin G Neel
- Laura and Isaac Perlmutter Cancer Center, NYU-Langone Medical Center, New York, New York
| | - Anniina Farkkila
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital; Department of Surgery, Harvard Medical School, Boston, Massachusetts.
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Massachusetts Institute of Technology Ludwig Center for Molecular Oncology, Cambridge, Massachusetts
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Abstract
MOTIVATION Gaining a comprehensive understanding of the genetics underlying cancer development and progression is a central goal of biomedical research. Its accomplishment promises key mechanistic, diagnostic and therapeutic insights. One major step in this direction is the identification of genes that drive the emergence of tumors upon mutation. Recent advances in the field of computational biology have shown the potential of combining genetic summary statistics that represent the mutational burden in genes with biological networks, such as protein-protein interaction networks, to identify cancer driver genes. Those approaches superimpose the summary statistics on the nodes in the network, followed by an unsupervised propagation of the node scores through the network. However, this unsupervised setting does not leverage any knowledge on well-established cancer genes, a potentially valuable resource to improve the identification of novel cancer drivers. RESULTS We develop a novel node embedding that enables classification of cancer driver genes in a supervised setting. The embedding combines a representation of the mutation score distribution in a node's local neighborhood with network propagation. We leverage the knowledge of well-established cancer driver genes to define a positive class, resulting in a partially labeled dataset, and develop a cross-validation scheme to enable supervised prediction. The proposed node embedding followed by a supervised classification improves the predictive performance compared with baseline methods and yields a set of promising genes that constitute candidates for further biological validation. AVAILABILITY AND IMPLEMENTATION Code available at https://github.com/BorgwardtLab/MoProEmbeddings. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anja C Gumpinger
- Department of Biosystems Science and Engineering, Machine Learning and Computational Biology Lab, ETH Zürich, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, Machine Learning and Computational Biology Lab, ETH Zürich, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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Saatcioglu HD, Kano M, Horn H, Zhang L, Samore W, Nagykery N, Meinsohn MC, Hyun M, Suliman R, Poulo J, Hsu J, Sacha C, Wang D, Gao G, Lage K, Oliva E, Morris Sabatini ME, Donahoe PK, Pépin D. Single-cell sequencing of neonatal uterus reveals an Misr2+ endometrial progenitor indispensable for fertility. eLife 2019; 8:46349. [PMID: 31232694 PMCID: PMC6650247 DOI: 10.7554/elife.46349] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 02/25/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
The Mullerian ducts are the anlagen of the female reproductive tract, which regress in the male fetus in response to MIS. This process is driven by subluminal mesenchymal cells expressing Misr2, which trigger the regression of the adjacent Mullerian ductal epithelium. In females, these Misr2+ cells are retained, yet their contribution to the development of the uterus remains unknown. Here, we report that subluminal Misr2+ cells persist postnatally in the uterus of rodents, but recede by week 37 of gestation in humans. Using single-cell RNA sequencing, we demonstrate that ectopic postnatal MIS administration inhibits these cells and prevents the formation of endometrial stroma in rodents, suggesting a progenitor function. Exposure to MIS during the first six days of life, by inhibiting specification of the stroma, dysregulates paracrine signals necessary for uterine development, eventually resulting in apoptosis of the Misr2+ cells, uterine hypoplasia, and complete infertility in the adult female. In the womb, mammals possess all of the preliminary sexual structures necessary to become either male or female. This includes the Mullerian duct, which develops into the Fallopian tubes, uterus, cervix, and vagina in female fetuses. In male fetuses, the testis secretes a hormone called Mullerian inhibiting substance (MIS). This triggers the activity of a small group of cells, known as Misr2+ cells, that cause the Mullerian duct to degenerate, preventing males from developing female sexual organs. It was not clear what happens to Misr2+ cells in female fetuses or if they affect how the uterus develops. Saatcioglu et al. now show that in newborn female mice and rats, a type of Misr2+ cell that sits within a thin inner layer of the developing uterus still responds to MIS. At this time, the uterus is in a critical early period of development. Treating the mice and rats with MIS protein during their first six days of life eventually caused the Misr2+ cells to die. The treatment also prevented a layer of connective tissue, known as the endometrial stroma, from forming in the uterus. As a result, the mice and rats were infertile and had severely underdeveloped uteri. While the Misr2+ cells are present in newborn rats and mice, Saatcioglu et al. found that they disappeared before birth in humans. However, the overall results suggest that Misr2+ cells act as progenitor cells that develop into the cells of the endometrial stroma. Future work could investigate the roles these cells play in causing uterine developmental disorders and infertility disorders. Furthermore, the finding that MIS inhibits the Misr2+ cells could help researchers to develop treatments for uterine cancer and other conditions where the cells of the uterus grow and divide too much.
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Affiliation(s)
- Hatice Duygu Saatcioglu
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Motohiro Kano
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Heiko Horn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Lihua Zhang
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Wesley Samore
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Nicholas Nagykery
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Marie-Charlotte Meinsohn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Minsuk Hyun
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Rana Suliman
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Joy Poulo
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jennifer Hsu
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Caitlin Sacha
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, United States
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, United States
| | - Kasper Lage
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Mary E Morris Sabatini
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
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Schuhmann S, Simkins J, Schork N, Codd S, Seymour J, Heijnen M, Saravia F, Horn H, Nirschl H, Guthausen G. Characterization and quantification of structure and flow in multichannel polymer membranes by MRI. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2018.10.072] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cuny L, Hille-Reichel A, Ödman P, Horn H. Untersuchung des Potenzials von produktiven Biofilmen anhand der Milchsäureproduktion. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855285] [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: 11/10/2022]
Affiliation(s)
- L. Cuny
- Karlsruher Institut für Technologie; Engler-Bunte-Institut, Wasserchemie und Wassertechnologie; Kaiserstraße 12 76131 Karlsruhe Deutschland
| | - A. Hille-Reichel
- Karlsruher Institut für Technologie; Engler-Bunte-Institut, Wasserchemie und Wassertechnologie; Kaiserstraße 12 76131 Karlsruhe Deutschland
| | - P. Ödman
- BASF SE; Carl-Bosch-Straße 38 67056 Ludwigshafen am Rhein Deutschland
| | - H. Horn
- Karlsruher Institut für Technologie; Engler-Bunte-Institut, Wasserchemie und Wassertechnologie; Kaiserstraße 12 76131 Karlsruhe Deutschland
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Fröschle M, Horn H, Spring O. Characterization of Jatropha curcas honeys originating from the southern highlands of Madagascar. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. GeNets: a unified web platform for network-based genomic analyses. Nat Methods 2018; 15:543-546. [PMID: 29915188 PMCID: PMC6450090 DOI: 10.1038/s41592-018-0039-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/02/2018] [Indexed: 11/25/2022]
Abstract
Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to quantitatively compare the signal-to-noise ratio of different networks, the biology they describe, and to identify the optimal network to interpret a particular genetic dataset. Via GeNets users can train a machine-learning model (Quack) to make such comparisons; and they can execute, store, and share analyses of genetic and RNA sequencing datasets.
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Affiliation(s)
- Taibo Li
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Electrical Engineering & Computer Science, MIT, Cambridge, MA, USA.,Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - April Kim
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Rosenbluh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Liraz Greenfeld
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David An
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Zimmer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jon Bistline
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Statistics, Harvard University, Cambridge, MA, USA
| | | | - Rajiv Narayan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Ted Liefeld
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bang Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dawn Thompson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah Calvo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jesse Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jake Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill Mesirov
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, USA
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Surgery, Harvard Medical School, Boston, MA, USA. .,Institute for Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Roskilde, Denmark.
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11
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Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K. NetSig: network-based discovery from cancer genomes. Nat Methods 2018; 15:61-66. [PMID: 29200198 PMCID: PMC5985961 DOI: 10.1038/nmeth.4514] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022]
Abstract
Methods that integrate molecular network information and tumor genome data could complement gene-based statistical tests to identify likely new cancer genes; but such approaches are challenging to validate at scale, and their predictive value remains unclear. We developed a robust statistic (NetSig) that integrates protein interaction networks with data from 4,742 tumor exomes. NetSig can accurately classify known driver genes in 60% of tested tumor types and predicts 62 new driver candidates. Using a quantitative experimental framework to determine in vivo tumorigenic potential in mice, we found that NetSig candidates induce tumors at rates that are comparable to those of known oncogenes and are ten-fold higher than those of random genes. By reanalyzing nine tumor-inducing NetSig candidates in 242 patients with oncogene-negative lung adenocarcinomas, we find that two (AKT2 and TFDP2) are significantly amplified. Our study presents a scalable integrated computational and experimental workflow to expand discovery from cancer genomes.
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Affiliation(s)
- Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Candace R. Chouinard
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Yashaswi Shrestha
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Jessica Xin Hu
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Elizabeth Worstell
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Emily Shea
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alireza Kashani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - William C. Hahn
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joshua D. Campbell
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Jesse S. Boehm
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
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12
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Zamò A, Pischimarov J, Schlesner M, Rosenstiel P, Bomben R, Horn H, Grieb T, Nedeva T, López C, Haake A, Richter J, Trümper L, Lawerenz C, Klapper W, Möller P, Hummel M, Lenze D, Szczepanowski M, Flossbach L, Schreder M, Gattei V, Ott G, Siebert R, Rosenwald A, Leich E. Differences between BCL2-break positive and negative follicular lymphoma unraveled by whole-exome sequencing. Leukemia 2017; 32:685-693. [PMID: 28824170 DOI: 10.1038/leu.2017.270] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022]
Abstract
Depending on disease stage follicular lymphoma (FL) lack the t(14;18) in ~15-~50% of cases. Nevertheless, most of these cases express BCL2. To elucidate mechanisms triggering BCL2 expression and promoting pathogenesis in t(14;18)-negative FL, exonic single-nucleotide variant (SNV) profiles of 28 t(14;18)-positive and 13 t(14;18)-negative FL were analyzed, followed by the integration of copy-number changes, copy-neutral LOH and published gene-expression data as well as the assessment of immunoglobulin N-glycosylation sites. Typical FL mutations also affected t(14;18)-negative FL. Curated gene set/pathway annotation of genes mutated in either t(14;18)-positive or t(14;18)-negative FL revealed a strong enrichment of same or similar gene sets but also a more prominent or exclusive enrichment of immune response and N-glycosylation signatures in t(14;18)-negative FL. Mutated genes showed high BCL2 association in both subgroups. Among the genes mutated in t(14;18)-negative FL 555 were affected by copy-number alterations and/or copy-neutral LOH and 96 were differently expressed between t(14;18)-positive and t(14;18)-negative FL (P<0.01). N-glycosylation sites were detected considerably less frequently in t(14;18)-negative FL. These results suggest a diverse portfolio of genetic alterations that may induce or regulate BCL2 expression or promote pathogenesis of t(14;18)-negative FL as well as a less specific but increased crosstalk with the microenvironment that may compensate for the lack of N-glycosylation.
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Affiliation(s)
- A Zamò
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - J Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schlesner
- Theoretical Bioinformatics (B080), Computational Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - R Bomben
- Department of Translational Research, CRO, Aviano, Italy
| | - H Horn
- Dr Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Stuttgart, Germany
| | - T Grieb
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - T Nedeva
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - C López
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Haake
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - J Richter
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Trümper
- Department of Hematology and Medical Oncology, University Hospital, Göttingen, Germany
| | - C Lawerenz
- Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - W Klapper
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - P Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - M Hummel
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - M Szczepanowski
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Flossbach
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schreder
- Medizinische Klinik und Poliklinik II, University Hospital Würzburg, Würzburg, Germany
| | - V Gattei
- Department of Translational Research, CRO, Aviano, Italy
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - R Siebert
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - E Leich
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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13
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Pérez-Palma E, Helbig I, Klein KM, Anttila V, Horn H, Reinthaler EM, Gormley P, Ganna A, Byrnes A, Pernhorst K, Toliat MR, Saarentaus E, Howrigan DP, Hoffman P, Miquel JF, De Ferrari GV, Nürnberg P, Lerche H, Zimprich F, Neubauer BA, Becker AJ, Rosenow F, Perucca E, Zara F, Weber YG, Lal D. Heterogeneous contribution of microdeletions in the development of common generalised and focal epilepsies. J Med Genet 2017; 54:598-606. [PMID: 28756411 PMCID: PMC5574393 DOI: 10.1136/jmedgenet-2016-104495] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 11/27/2022]
Abstract
Background Microdeletions are known to confer risk to epilepsy, particularly at genomic rearrangement ‘hotspot’ loci. However, microdeletion burden not overlapping these regions or within different epilepsy subtypes has not been ascertained. Objective To decipher the role of microdeletions outside hotspots loci and risk assessment by epilepsy subtype. Methods We assessed the burden, frequency and genomic content of rare, large microdeletions found in a previously published cohort of 1366 patients with genetic generalised epilepsy (GGE) in addition to two sets of additional unpublished genome-wide microdeletions found in 281 patients with rolandic epilepsy (RE) and 807 patients with adult focal epilepsy (AFE), totalling 2454 cases. Microdeletions were assessed in a combined and subtype-specific approaches against 6746 controls. Results When hotspots are considered, we detected an enrichment of microdeletions in the combined epilepsy analysis (adjusted p=1.06×10−6,OR 1.89, 95% CI 1.51 to 2.35). Epilepsy subtype-specific analyses showed that hotspot microdeletions in the GGE subgroup contribute most of the overall signal (adjusted p=9.79×10−12, OR 7.45, 95% CI 4.20–13.5). Outside hotspots , microdeletions were enriched in the GGE cohort for neurodevelopmental genes (adjusted p=9.13×10−3,OR 2.85, 95% CI 1.62–4.94). No additional signal was observed for RE and AFE. Still, gene-content analysis identified known (NRXN1, RBFOX1 and PCDH7) and novel (LOC102723362) candidate genes across epilepsy subtypes that were not deleted in controls. Conclusions Our results show a heterogeneous effect of recurrent and non-recurrent microdeletions as part of the genetic architecture of GGE and a minor contribution in the aetiology of RE and AFE.
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Affiliation(s)
- Eduardo Pérez-Palma
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany.,Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Karl Martin Klein
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Verneri Anttila
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Padhraig Gormley
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Ganna
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrea Byrnes
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Mohammad R Toliat
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Elmo Saarentaus
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel P Howrigan
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Per Hoffman
- Division of Medical Genetics Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Juan Francisco Miquel
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research,University of Tübingen, Tübingen, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Bern A Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Albert J Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Felix Rosenow
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Emilio Perucca
- C. Mondino National Neurological Institute, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Federico Zara
- Laboratory of Neurogenetics, Neuromuscular Disease Unit, Genova, Italy
| | - Yvonne G Weber
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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14
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Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K. Abstract 5567: A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5567] [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
High throughput sequencing has revolutionized the study of the cancer genome, enabling numerous discoveries in basic and clinical research. However, considerable sample sizes are required to find cancer driver genes with intermediate and low mutation frequencies, and for a large proportion of patients the molecular cause (e.g. driver gene(s)) of disease is unknown. Here, we describe an integrated computational and experimental workflow that combines cancer genome data, molecular network information, multiplexed in vivo tumorigenesis assays, and reanalysis of driver-gene-negative cancer patients to predict and validate new driver genes. We develop a statistic, network mutation burden, that combines molecular network information with data from 4,742 cancer genomes to accurately classify known driver genes across 21 tumor types and predict 62 driver gene candidates.Of these, 35 gene candidates were tested in multiplexed in vivo tumorigenesis cell assays using sensitized immortalized human embryonic kidney (HA1E-M) and immortalized human lung epithelial (SALE-Y) cell lines.Tumor formation in vivo was observed for 11 genes (2 in HA1E-M, 3 in SALE-Y, 6 in both). By reanalyzing 242 lung adenocarcinoma patients with an unknown molecular cause of disease we show that two of these candidates, TFDP2 and AKT2, are significantly amplified in multiple samples.Overall, we describe a scalable combined computational and experimental framework to predict and validate driver genes across many tumor types. Our proof-of-concept approach should become increasingly useful as the number of cancer genomes continues to grow.
Citation Format: Heiko Horn, Michael S. Lawrence, Candace R. Chouinard, Yashaswi Shrestha, Jessica Xin Hu, Elizabeth Worstell, Emily Shea, Nina Ilic, Eejung Kim, Atanas Kamburov, Alireza Kashani, William C. Hahn, Joshua D. Campbell, Jesse S. Boehm, Gad Getz, Kasper Lage. A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5567. doi:10.1158/1538-7445.AM2017-5567
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Affiliation(s)
- Heiko Horn
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | | | | | - Emily Shea
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | - Nina Ilic
- 4Dana-Farber Cancer Institute, Boston, MA
| | - Eejung Kim
- 4Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Gad Getz
- 5Massachusetts General Hospital, Boston, MA
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15
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Kühnl A, Cunningham D, Counsell N, Hawkes EA, Qian W, Smith P, Chadwick N, Lawrie A, Mouncey P, Jack A, Pocock C, Ardeshna KM, Radford J, McMillan A, Davies J, Turner D, Kruger A, Johnson PW, Gambell J, Rosenwald A, Ott G, Horn H, Ziepert M, Pfreundschuh M, Linch D. Outcome of elderly patients with diffuse large B-cell lymphoma treated with R-CHOP: results from the UK NCRI R-CHOP14v21 trial with combined analysis of molecular characteristics with the DSHNHL RICOVER-60 trial. Ann Oncol 2017; 28:1540-1546. [PMID: 28398499 PMCID: PMC5815562 DOI: 10.1093/annonc/mdx128] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND There is an on-going debate whether 2- or 3-weekly administration of R-CHOP is the preferred first-line treatment for elderly patients with diffuse large B-cell lymphoma (DLBCL). The UK NCRI R-CHOP14v21 randomized phase 3 trial did not demonstrate a difference in outcomes between R-CHOP-14 and R-CHOP-21 in newly diagnosed DLBCL patients aged 19-88 years, but data on elderly patients have not been reported in detail so far. Here, we provide a subgroup analysis of patients ≥60 years treated on the R-CHOP14v21 trial with extended follow-up. PATIENTS AND METHODS Six hundred and four R-CHOP14v21 patients ≥60 years were included in this subgroup analysis, with a median follow-up of 77.7 months. To assess the impact of MYC rearrangements (MYC-R) and double-hit-lymphoma (DHL) on outcome in elderly patients, we performed a joint analysis of cases with available molecular data from the R-CHOP14v21 (N = 217) and RICOVER-60 (N = 204) trials. RESULTS Elderly DLBCL patients received high dose intensities with median total doses of ≥98% for all agents. Toxicities were similar in both arms with the exception of more grade ≥3 neutropenia (P < 0.0001) and fewer grade ≥3 thrombocytopenia (P = 0.05) in R-CHOP-21 versus R-CHOP-14. The elderly patient population had a favorable 5-year overall survival (OS) of 69% (95% CI: 65-73). We did not identify any subgroup of patients that showed differential response to either regimen. In multivariable analysis including individual factors of the IPI, gender, bulk, B2M and albumin levels, only age and B2M were of independent prognostic significance for OS. Molecular analyses demonstrated a significant impact of MYC-R (HR = 1.96; 95% CI: 1.22-3.16; P = 0.01) and DHL (HR = 2.21; 95% CI: 1.18-4.11; P = 0.01) on OS in the combined trial cohorts, independent of other prognostic factors. CONCLUSIONS Our data support equivalence of both R-CHOP application forms in elderly DLBCL patients. Elderly MYC-R and DHL patients have inferior prognosis and should be considered for alternative treatment approaches. TRIAL NUMBERS ISCRTN 16017947 (R-CHOP14v21); NCT00052936 (RICOVER-60).
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MESH Headings
- Age Factors
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Murine-Derived/administration & dosage
- Antibodies, Monoclonal, Murine-Derived/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Biomarkers, Tumor/genetics
- Cyclophosphamide/administration & dosage
- Cyclophosphamide/adverse effects
- Doxorubicin/administration & dosage
- Doxorubicin/adverse effects
- Drug Administration Schedule
- Female
- Gene Rearrangement
- Humans
- Kaplan-Meier Estimate
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Multivariate Analysis
- Patient Selection
- Precision Medicine
- Prednisone/administration & dosage
- Prednisone/adverse effects
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-6/genetics
- Proto-Oncogene Proteins c-myc/genetics
- Risk Factors
- Rituximab
- Time Factors
- Treatment Outcome
- United Kingdom
- Vincristine/administration & dosage
- Vincristine/adverse effects
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Affiliation(s)
- A. Kühnl
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London and Surrey
| | - D. Cunningham
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London and Surrey
| | - N. Counsell
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - E. A. Hawkes
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London and Surrey
- Olivia-Newton John Cancer Research & Wellness Centre, Melbourne, Australia
| | - W. Qian
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge
| | - P. Smith
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - N. Chadwick
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - A. Lawrie
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - P. Mouncey
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - A. Jack
- HMDS, St James’s Institute of Oncology, Leeds
| | | | - K. M. Ardeshna
- Department of Hematology, University College London, London
- Mount Vernon Cancer Centre, Northwood
| | - J. Radford
- Department of Medical Oncology, University of Manchester and the Christie NHS Foundation Trust, Manchester
| | - A. McMillan
- Department of Hematology, Nottingham City Hospital, Nottingham
| | | | - D. Turner
- Department of Hematology, Torbay Hospital, Torquay
| | | | - P. W. Johnson
- Cancer Research UK Center, University of Southampton, Southampton, UK
| | - J. Gambell
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | - A. Rosenwald
- Institute of Pathology, Würzburg University, Würzburg
| | - G. Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart
| | - H. Horn
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart and University of Tübingen, Stuttgart
| | - M. Ziepert
- Institute for Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig
| | - M. Pfreundschuh
- Department of Medicine, Saarland University Medical School, Homburg/Saar, Germany
| | - D. Linch
- Department of Hematology, University College London, London
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16
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Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K. A scored human protein-protein interaction network to catalyze genomic interpretation. Nat Methods 2017; 14:61-64. [PMID: 27892958 PMCID: PMC5839635 DOI: 10.1038/nmeth.4083] [Citation(s) in RCA: 369] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023]
Abstract
Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (InWeb_InBioMap, or InWeb_IM) with severalfold more interactions (>500,000) and better functional biological relevance than comparable resources. We illustrate that InWeb_InBioMap enables functional interpretation of >4,700 cancer genomes and genes involved in autism.
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Affiliation(s)
- Taibo Li
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rasmus Wernersson
- Intomics A/S, Lyngby, Denmark
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | | | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Johnathan Mercer
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Greg Slodkowicz
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Olga Rigina
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Hans H Stærfeldt
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Institute for Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Roskilde, Denmark
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17
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Cantisani A, Stegmayer K, Bracht T, Federspiel A, Wiest R, Horn H, Müller TJ, Schneider C, Höfle O, Strik W, Walther S. Distinct resting-state perfusion patterns underlie psychomotor retardation in unipolar vs. bipolar depression. Acta Psychiatr Scand 2016; 134:329-38. [PMID: 27497085 DOI: 10.1111/acps.12625] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Psychomotor abnormalities characterize both unipolar (UP) depression and bipolar (BP) depression. We aimed to assess their neurobiological correlates in terms of motor activity (AL) and resting-state cerebral blood flow (rCBF) and investigate their association in BP, UP, and healthy controls (HC). METHOD We enrolled 42 depressed patients (22 BP, 20 UP) and 19 HC matched for age, gender, education, income. AL and rCBF were objectively assessed with the use of wrist actigraphy and arterial spin labeling. Group differences and the association of AL and rCBF were computed. RESULTS Activity level was significantly reduced in patients, but no difference was found between BP and UP. Increased perfusion was found in BP compared with UP and HC, in multiple brain areas. We found positive correlations of rCBF and AL in BP and UP, in different parts of the insula and frontal regions. Only BP showed a cluster in the left precentral gyrus. In HC, only inverse correlations of AL and rCBF were found. CONCLUSION The differences in rCBF and in the localization of the clusters of positive AL/rCBF correlations between BP and UP suggest that different neural impairments may underlie motor symptoms in the two disorders, but finally converge in phenotypically similar manifestations.
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Affiliation(s)
- A Cantisani
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland. , .,NeuroFarBa Department, University of Florence, Florence, Italy. ,
| | - K Stegmayer
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - T Bracht
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - A Federspiel
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - R Wiest
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Bern, Bern, Switzerland
| | - H Horn
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - T J Müller
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - C Schneider
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - O Höfle
- Department of Neurology, University Hospital Bern, Bern, Switzerland
| | - W Strik
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
| | - S Walther
- Translational Research Center, University Hospital of Psychiatry, Bern, Switzerland
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18
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Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers. Cell Syst 2016; 3:302-316.e4. [PMID: 27684187 PMCID: PMC5455996 DOI: 10.1016/j.cels.2016.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/11/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022]
Abstract
Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches. We interrogated 177 genes that we classified as essential for the proliferation of cancer cells exhibiting constitutive β-catenin activity and integrated data for each of the candidates, derived from orthogonal short hairpin RNA (shRNA) knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated gene editing knockout screens, to yield 69 validated genes. We then characterized the relationships between sets of these genes using complementary assays: medium-throughput stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry, yielding 3,639 protein-protein interactions, and a CRISPR-mediated pairwise double knockout screen, yielding 375 combinations exhibiting greater- or lesser-than-additive phenotypic effects indicating genetic interactions. These studies identify previously unreported regulators of β-catenin, define functional networks required for the survival of β-catenin-active cancers, and provide an experimental strategy that may be applied to define other signaling networks.
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Affiliation(s)
- Joseph Rosenbluh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Johnathan Mercer
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yashaswi Shrestha
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Rachel Oliver
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Pablo Tamayo
- Moores Cancer Center and School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Itay Tirosh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ella Hartenian
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Heiko Horn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lola Fagbami
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jacob Jaffe
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Kasper Lage
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA.
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19
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Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov 2016; 6:714-26. [PMID: 27147599 DOI: 10.1158/2159-8290.cd-16-0160] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/26/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies. SIGNIFICANCE Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Lihua Zou
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Xiaoping Yang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rakela Lubonja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Cindy Nguyen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medicine, University of California, San Diego, La Jolla, California
| | - Heiko Horn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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20
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Pepin D, Sosulski A, Horn H, Zhang L, Coletti C, Vathipadiekal V, Castro CM, Birrer MJ, Nagano O, Saya H, Lage K, Donahoe PK. Abstract B26: Cell surface expression of CD44v8-10 is associated with good prognosis while cleaved extracellular domain is a marker of poor prognosis in high-grade serous epithelial ovarian cancer. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.ovca15-b26] [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
CD44 is a transmembrane hyaluronic acid receptor gene that encodes over 100 different tissue specific protein isoforms. The most prevalent, standard CD44 (CD44s), has been used as one of a panel of markers identifying a stem cell enriched population in ovarian cancer. While expression of the CD44 epithelial specific variant containing exons v810 (CD44v810) has been associated with more resistant and metastatic tumors in gastrointestinal and breast cancers, its role in highgrade serous ovarian cancer is unknown. The gene expression profiles from a cohort of 254 tumor samples, of The Cancer Genome Atlas RNAseqV2 ovarian serous cystadenocarcinoma collection, were analyzed for expression of different CD44 isoforms. A trend for longer survival was observed in patients with tumors with high expression of CD44 isoforms that include exons V8-10. Immunohistochemical analysis of tumors using an antibody recognizing CD44v810 (rat antiCD44v9 RV3) was performed on an independent cohort of 210 patients with high-grade serous ovarian cancer using a tumor tissue microarray. Patient stratification based on unbiased software analysis of staining revealed a statistically significant increase in survival in patients with the highest levels of protein expression compared to those with the lowest expression with a median survival time in the top 10% of 1203 days versus 751 days for the bottom 10% (p= 0.001). Immunohistochemical expression of CD44v810 transmembrane protein in primary ovarian cancer cell lines was correlated with a predominantly epithelial phenotype characterized by high expression of epithelial markers and low expression of mesenchymal markers by principal component analysis. Conversely, detection of proteolytically cleaved and secreted extracellular domain of CD44v810 (solCD44v810) in patient ascites samples was correlated with significantly worse prognosis. Therefore, presence of transmembrane CD44v8-10 on the surface of primary tumor cells may be a marker of a highly epithelial tumor with better prognosis while enzymatic cleavage of CD44v8-10, as detected by presence of the soluble extracellular domain in ascites fluid, may be indicative of a more metastatic disease with worse prognosis.
Citation Format: David Pepin, Amanda Sosulski, Heiko Horn, Lihua Zhang, Caroline Coletti, vinod Vathipadiekal, Cesar M. Castro, Michael J. Birrer, Osamu Nagano, Hidekuyi Saya, Kasper Lage, Patricia K. Donahoe. Cell surface expression of CD44v8-10 is associated with good prognosis while cleaved extracellular domain is a marker of poor prognosis in high-grade serous epithelial ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B26.
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Affiliation(s)
- David Pepin
- 1Massachusetts General Hospital, Boston, MA,
| | | | - Heiko Horn
- 1Massachusetts General Hospital, Boston, MA,
| | - Lihua Zhang
- 1Massachusetts General Hospital, Boston, MA,
| | | | | | | | | | - Osamu Nagano
- 2Keio University School of Medicine, Tokyo, Japan
| | | | - Kasper Lage
- 1Massachusetts General Hospital, Boston, MA,
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21
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Labena A, Hegazy MA, Horn H, Müller E. Sulfidogenic-corrosion inhibitory effect of cationic monomeric and gemini surfactants: planktonic and sessile diversity. RSC Adv 2016. [DOI: 10.1039/c6ra02393b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A cationic monomeric surfactant (CMS) and a cationic gemini surfactant (CGS) were successfully synthesized and characterized. Both surfactants prevent sulfidogenic activity in bulk phase and on metal surface (biofilms) at a salinity of 3.18% NaCl.
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Affiliation(s)
- A. Labena
- Technical University of Munich
- Urban Water Systems Engineering
- 85748 Garching
- Germany
| | - M. A. Hegazy
- Egyptian Petroleum Research Institute (EPRI)
- Cairo
- Egypt
| | - H. Horn
- Karlsruhe Institute of Technology
- Engler-Bunte-Institut
- Water Chemistry and Water Technology
- 76121 Karlsruhe
- Germany
| | - E. Müller
- Technical University of Munich
- Urban Water Systems Engineering
- 85748 Garching
- Germany
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22
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Gmurek M, Horn H, Majewsky M. Phototransformation of sulfamethoxazole under simulated sunlight: Transformation products and their antibacterial activity toward Vibrio fischeri. Sci Total Environ 2015; 538:58-63. [PMID: 26298248 DOI: 10.1016/j.scitotenv.2015.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Sulfamethoxazole (SMX) is a bacteriostatic antibiotic ubiquitously found in the aquatic environment. Since conventional biological wastewater treatment is not efficient to remove SMX, photolysis in natural waters can represent an important transformation pathway. It was recently shown that SMX transformation products can retain antibiotic activity. Therefore, it is crucial to better understand photochemical processes occurring in natural water just as the formation of active transformation products (TPs). During long-term SMX photolysis experiments (one week), nine TPs were identified by reference standards. Moreover, five further TPs of photodecomposition of SMX were found. For the first time, a TP with m/z 271 [M+H](+) was observed during photolysis and tentatively confirmed as 4,x-dihydroxylated SMX. The DOC mass balance clearly showed that only around 5 to 10% were mineralized during the experiment emphasizing the need to elucidate the fate of TPs. Bacterial bioassays confirmed that the mixture retains its antibiotic toxicity toward luminescence (24h) and that there is no change over the treatment time on EC50. In contrast, growth inhibition activity was found to slightly decrease over the irradiation time. However, this decrease was not proportional to the transformation of the parent compound SMX.
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Affiliation(s)
- M Gmurek
- Lodz University of Technology, Faculty of Process & Environmental Engineering, Department of Bioprocess Engineering, Wolczanska 213, 90-924 Lodz, Poland.
| | - H Horn
- Karlsruhe Institute of Technology (KIT), Engler-Bunte-Institut, Chair of Water Chemistry and Water Technology, Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
| | - M Majewsky
- Karlsruhe Institute of Technology (KIT), Engler-Bunte-Institut, Chair of Water Chemistry and Water Technology, Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany
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23
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Leich E, Hoster E, Wartenberg M, Unterhalt M, Siebert R, Koch K, Klapper W, Engelhard M, Puppe B, Horn H, Staiger AM, Stuhlmann-Laeisz C, Bernd HW, Feller AC, Hummel M, Lenze D, Stein H, Hartmann S, Hansmann ML, Möller P, Hiddemann W, Dreyling M, Ott G, Rosenwald A. Similar clinical features in follicular lymphomas with and without breaks in the BCL2 locus. Leukemia 2015; 30:854-60. [PMID: 26621338 DOI: 10.1038/leu.2015.330] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/05/2015] [Accepted: 11/13/2015] [Indexed: 01/18/2023]
Abstract
Approximately 15% of follicular lymphomas (FLs) lack breaks in the BCL2 locus. The aim of this study was to better define molecular and clinical features of BCL2-breakpoint/t(14;18)-negative FLs. We studied the presence of BCL2, BCL6 and MYC breaks by fluorescence in situ hybridization and the expression of BCL2, MUM1, CD10, P53 and Ki67 in large clinical trial cohorts of 540 advanced-stage FL cases and 116 early-stage disease FL patients treated with chemotherapy regimens and radiation, respectively. A total of 86% and 53% of advanced- and early-stage FLs were BCL2-breakpoint-positive, respectively. BCL2 was expressed in almost all FLs with BCL2 break and also in 86% and 69% of BCL2-breakpoint-negative advanced- and early-stage FLs, respectively. CD10 expression was significantly reduced in BCL2-breakpoint-negative FLs of all stages and MUM1 and Ki67 expression were significantly increased in BCL2-break-negative early-stage FLs. Patient characteristics did not differ between FLs with and without BCL2 breaks and neither did survival times in advanced-stage FLs. These results suggest that the molecular profile differs to some extent between FLs with and without BCL2 breaks and support the notion that FLs with and without BCL2 breaks belong to the same lymphoma entity.
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Affiliation(s)
- E Leich
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
| | - E Hoster
- Institute of Medical Informatics, Biometry, and Epidemiology, University of Munich, Munich, Germany
| | - M Wartenberg
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
| | - M Unterhalt
- Department of Internal Medicine III, University Hospital Munich, Munich, Germany
| | - R Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - K Koch
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, Germany
| | - W Klapper
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Engelhard
- Department for Radiotherapy, University Hospital Essen, Essen, Germany
| | - B Puppe
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
| | - H Horn
- Margarete Fischer-Bosch Institute of Clinical Pharmacology, Robert-Bosch-Krankenhaus, Stuttgart and University of Tübingen, Tübingen, Germany
| | - A M Staiger
- Margarete Fischer-Bosch Institute of Clinical Pharmacology, Robert-Bosch-Krankenhaus, Stuttgart and University of Tübingen, Tübingen, Germany
| | - C Stuhlmann-Laeisz
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - H W Bernd
- Institute of Pathology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - A C Feller
- Institute of Pathology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - M Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité Universitätsmedizin, Berlin, Germany
| | - D Lenze
- Institute of Pathology, Campus Benjamin Franklin, Charité Universitätsmedizin, Berlin, Germany
| | - H Stein
- Pathodiagnostik Berlin, Berlin, Germany
| | - S Hartmann
- Institute of Pathology, University Hospital Frankfurt am, Frankfurt, Germany
| | - M L Hansmann
- Institute of Pathology, University Hospital Frankfurt am, Frankfurt, Germany
| | - P Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - W Hiddemann
- Department of Internal Medicine III, University Hospital Munich, Munich, Germany
| | - M Dreyling
- Department of Internal Medicine III, University Hospital Munich, Munich, Germany
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
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24
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Sramek M, Woerz B, Horn H, Weiss J, Kohlus R. Preparation of High-Grade Powders from Honey-Glucose Syrup Formulations by Vacuum Foam-Drying Method. J FOOD PROCESS PRES 2015. [DOI: 10.1111/jfpp.12660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Sramek
- Department of Food Processing Engineering; Institute of Food Science and Biotechnology; Hohenheim University; Stuttgart Germany
| | - B. Woerz
- Department of Food Processing Engineering; Institute of Food Science and Biotechnology; Hohenheim University; Stuttgart Germany
| | - H. Horn
- Apicultural State Institute; Hohenheim University; Stuttgart Germany
| | - J. Weiss
- Department of Food Physics and Meat Science; Institute of Food Science and Biotechnology; Hohenheim University; Stuttgart Germany
| | - R. Kohlus
- Department of Food Processing Engineering; Institute of Food Science and Biotechnology; Hohenheim University; Stuttgart Germany
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25
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Emdal KB, Pedersen AK, Bekker-Jensen DB, Tsafou KP, Horn H, Lindner S, Schulte JH, Eggert A, Jensen LJ, Francavilla C, Olsen JV. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Sci Signal 2015; 8:ra40. [PMID: 25921289 DOI: 10.1126/scisignal.2005769] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SH-SY5Y neuroblastoma cells respond to nerve growth factor (NGF)-mediated activation of the tropomyosin-related kinase A (TrkA) with neurite outgrowth, thereby providing a model to study neuronal differentiation. We performed a time-resolved analysis of NGF-TrkA signaling in neuroblastoma cells using mass spectrometry-based quantitative proteomics. The combination of interactome, phosphoproteome, and proteome data provided temporal insights into the molecular events downstream of NGF binding to TrkA. We showed that upon NGF stimulation, TrkA recruits the E3 ubiquitin ligase Cbl-b, which then becomes phosphorylated and ubiquitylated and decreases in abundance. We also found that recruitment of Cbl-b promotes TrkA ubiquitylation and degradation. Furthermore, the amount of phosphorylation of the kinase ERK and neurite outgrowth increased upon Cbl-b depletion in several neuroblastoma cell lines. Our findings suggest that Cbl-b limits NGF-TrkA signaling to control the length of neurites.
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Affiliation(s)
- Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Anna-Kathrine Pedersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Kalliopi P Tsafou
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Heiko Horn
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany. Department of Pediatric Oncology and Hematology, Charité Berlin, Charitéplatz 1, 10117 Berlin, Germany. German Cancer Consortium (DKTK), 13353 Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany. Department of Pediatric Oncology and Hematology, Charité Berlin, Charitéplatz 1, 10117 Berlin, Germany. German Cancer Consortium (DKTK), 13353 Berlin, Germany
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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26
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Rocktäschel T, Klarmann C, Ochoa J, Boisson P, Sørensen K, Horn H. Influence of the granulation grade on the concentration of suspended solids in the effluent of a pilot scale sequencing batch reactor operated with aerobic granular sludge. Sep Purif Technol 2015. [DOI: 10.1016/j.seppur.2015.01.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Horn H, Ziepert M, Wartenberg M, Staiger AM, Barth TFE, Bernd HW, Feller AC, Klapper W, Stuhlmann-Laeisz C, Hummel M, Stein H, Lenze D, Hartmann S, Hansmann ML, Möller P, Cogliatti S, Pfreundschuh M, Trümper L, Loeffler M, Glass B, Schmitz N, Ott G, Rosenwald A. Different biological risk factors in young poor-prognosis and elderly patients with diffuse large B-cell lymphoma. Leukemia 2015; 29:1564-70. [DOI: 10.1038/leu.2015.43] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 02/02/2023]
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28
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Labena A, Hegazy M, Horn H, Müller E. The biocidal effect of a novel synthesized gemini surfactant on environmental sulfidogenic bacteria: Planktonic cells and biofilms. Materials Science and Engineering: C 2015; 47:367-75. [DOI: 10.1016/j.msec.2014.10.079] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/10/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
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Grueters U, Seltmann T, Schmidt H, Horn H, Pranchai A, Vovides A, Peters R, Vogt J, Dahdouh-Guebas F, Berger U. The mangrove forest dynamics model mesoFON. Ecol Modell 2014. [DOI: 10.1016/j.ecolmodel.2014.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nel CPG, Schoeman LC, Van Wyngaardt M, Horn H, Goedhals L, Joubert G. The prevalence of HIV amongst women with cervix cancer. S Afr Fam Pract (2004) 2014. [DOI: 10.1080/20786204.2006.10873334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Abstract
Die Acidolyse von Tetraorganoplumbanen PbR4 mit verschiedenen aciden Verbindungen HX (z. B. CH3COOH, CF3COOH, CCl3COOH, C (CH3)3COOH) wurde hinsichtlich des Einflusses der Reste R und der Acidität von HX auf die präparative Anwendbarkeit dieser Reaktion zur Darstellung von R3PbX und/bzw. R2PbX2 untersucht.
Tetraphenylplumban reagierte in allen Fällen deutlich schneller mit HX als Tetraalkylplumbane.
Mit Trifluoressigsäure ließen sich (alkyl) 3PbX, (alkyl) 2PbX2 und (C8H5) 2PbX2, nicht jedoch (C6H5) 3PbX gewinnen.
Trimethylessigsäure reagiert mit Pb (alkyl) 4 so langsam, daß Zersetzungsreaktionen überwogen und die Darstellung von hydrolysierbarem (!) (C2H5)2PbX2 nur unter SiO2-Katalyse gelang.
Pb (II) -Verbindungen entstanden in mehr oder weniger großer Menge besonders dann, wenn bei der Acidolyse Carbonsäuren bzw. deren Derivate oder HS-acide Verbindungen (C6H5SH, HOCH2CH2SH) eingesetzt wurden.
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Affiliation(s)
- F. Huber
- Institut für Anorganische Chemie und Elektrochemie der Technischen Hochschule Aachen
| | - H. Horn
- Institut für Anorganische Chemie und Elektrochemie der Technischen Hochschule Aachen
| | - H. J. Haupt
- Institut für Anorganische Chemie und Elektrochemie der Technischen Hochschule Aachen
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Bøgebo R, Horn H, Olsen JV, Gammeltoft S, Jensen LJ, Hansen JL, Christensen GL. Predicting kinase activity in angiotensin receptor phosphoproteomes based on sequence-motifs and interactions. PLoS One 2014; 9:e94672. [PMID: 24722691 PMCID: PMC3983226 DOI: 10.1371/journal.pone.0094672] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/17/2014] [Indexed: 01/14/2023] Open
Abstract
Recent progress in the understanding of seven-transmembrane receptor (7TMR) signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR) is one of the most studied 7TMRs with respect to selective activation of the β-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets.
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Affiliation(s)
- Rikke Bøgebo
- Department of Clinical Biochemistry, Glostrup Research Institute, Glostrup Hospital, Glostrup, Denmark
| | - Heiko Horn
- Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V. Olsen
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Steen Gammeltoft
- Department of Clinical Biochemistry, Glostrup Research Institute, Glostrup Hospital, Glostrup, Denmark
| | - Lars J. Jensen
- Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob L. Hansen
- Department of Biomedical Sciences and The Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (JLH); (GLC)
| | - Gitte L. Christensen
- Department of Clinical Biochemistry, Glostrup Research Institute, Glostrup Hospital, Glostrup, Denmark
- Cellular and Metabolic Research Section, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (JLH); (GLC)
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Abstract
Many protein domains bind to short peptide sequences, called linear motifs. Data on their sequence specificities is sparse, which is why biologists usually resort to basic pattern searches to identify new putative binding sites for experimental follow-up. Most motifs have poor specificity and prioritization of the matches is thus crucial when scanning a full proteome with a pattern. Here we present a generic method to prioritize motif occurrence predictions by using cellular contextual information. We take 2 parameters as input: the motif occurrences and one or more of the interacting domains. The potential hits are ranked based on how strongly the context network associates them with a protein containing one of the specified domains, which leads to an increased predictive performance. The method is available through a web interface at doremi.jensenlab.org, which allows for an easy application of the method. We show that this approach leads to improved predictions of binding partners for PDZ domains and the SUMO binding domain. This is consistent with the earlier observation that coupling sequence motifs with network information improves kinase-specific substrate predictions.
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Affiliation(s)
- Heiko Horn
- NNF Center for Protein Research, University of Copenhagen , Denmark
| | - Niall Haslam
- Complex and Adaptive Systems Laboratory, University College Dublin , Dublin , Ireland ; Conway Institute of Biomolecular and Biomedical Science, University College Dublin , Dublin , Ireland
| | - Lars Juhl Jensen
- NNF Center for Protein Research, University of Copenhagen , Denmark
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Falkenstern-Ge R, Kimmich M, Grabner A, Horn H, Friedel G, Ott G, Kohlhäufl M. Primäres Pulmonales Synovialsarkom – Ein Fallbericht. Pneumologie 2014. [DOI: 10.1055/s-0034-1367948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sylvestersen KB, Horn H, Jungmichel S, Jensen LJ, Nielsen ML. Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. Mol Cell Proteomics 2014; 13:2072-88. [PMID: 24563534 DOI: 10.1074/mcp.o113.032748] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The covalent attachment of methyl groups to the side-chain of arginine residues is known to play essential roles in regulation of transcription, protein function, and RNA metabolism. The specific N-methylation of arginine residues is catalyzed by a small family of gene products known as protein arginine methyltransferases; however, very little is known about which arginine residues become methylated on target substrates. Here we describe a proteomics methodology that combines single-step immunoenrichment of methylated peptides with high-resolution mass spectrometry to identify endogenous arginine mono-methylation (MMA) sites. We thereby identify 1027 site-specific MMA sites on 494 human proteins, discovering numerous novel mono-methylation targets and confirming the majority of currently known MMA substrates. Nuclear RNA-binding proteins involved in RNA processing, RNA localization, transcription, and chromatin remodeling are predominantly found modified with MMA. Despite this, MMA sites prominently are located outside RNA-binding domains as compared with the proteome-wide distribution of arginine residues. Quantification of arginine methylation in cells treated with Actinomycin D uncovers strong site-specific regulation of MMA sites during transcriptional arrest. Interestingly, several MMA sites are down-regulated after a few hours of transcriptional arrest. In contrast, the corresponding di-methylation or protein expression levels are not altered, confirming that MMA sites contain regulated functions on their own. Collectively, we present a site-specific MMA data set in human cells and demonstrate for the first time that MMA is a dynamic post-translational modification regulated during transcriptional arrest by a hitherto uncharacterized arginine demethylase.
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Affiliation(s)
- Kathrine B Sylvestersen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Heiko Horn
- §Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Stephanie Jungmichel
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lars J Jensen
- §Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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West S, Horn H, Hijnen W, Castillo C, Wagner M. Confocal laser scanning microscopy as a tool to validate the efficiency of membrane cleaning procedures to remove biofilms. Sep Purif Technol 2014. [DOI: 10.1016/j.seppur.2013.11.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Dengler MA, Weilbacher A, Gutekunst M, Staiger AM, Vöhringer MC, Horn H, Ott G, Aulitzky WE, van der Kuip H. Discrepant NOXA (PMAIP1) transcript and NOXA protein levels: a potential Achilles' heel in mantle cell lymphoma. Cell Death Dis 2014; 5:e1013. [PMID: 24457957 PMCID: PMC4040662 DOI: 10.1038/cddis.2013.552] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/12/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023]
Abstract
Mantle cell lymphoma (MCL) is an aggressive lymphoid neoplasm with transient response to conventional chemotherapy. We here investigated the role of the Bcl-2 homology domain 3-only protein NOXA for life–death decision in MCL. Surprisingly, NOXA (PMAIP1) mRNA and NOXA protein levels were extremely discrepant in MCL cells: NOXA mRNA was found to be highly expressed whereas NOXA protein levels were low. Chronic active B-cell receptor signaling and to a minor degree cyclin D1 overexpression contributed to high NOXA mRNA expression levels in MCL cells. The phoshatidyl-inositol-3 kinase/AKT/mammalian target of rapamycin pathway was identified as the major downstream signaling pathway involved in the maintenance of NOXA gene expression. Interestingly, MCL cells adapt to this constitutive pro-apoptotic signal by extensive ubiquitination and rapid proteasomal degradation of NOXA protein (T½∼15–30 min). In addition to the proteasome inhibitor Bortezomib, we identified the neddylation inhibitor MLN4924 and the fatty acid synthase inhibitor Orlistat as potent inducers of NOXA protein expression leading to apoptosis in MCL. All inhibitors targeted NOXA protein turnover. In contrast to Bortezomib, MLN4924 and Orlistat interfered with the ubiquitination process of NOXA protein thereby offering new strategies to kill Bortezomib-resistant MCL cells. Our data, therefore, highlight a critical role of NOXA in the balance between life and death in MCL. The discrepancy between NOXA transcript and protein levels is essential for sensitivity of MCL to ubiquitin-proteasome system inhibitors and could therefore provide a druggable Achilles' heel of MCL cells.
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Affiliation(s)
- M A Dengler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
| | - A Weilbacher
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
| | - M Gutekunst
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
| | - A M Staiger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
| | - M C Vöhringer
- Second Department of Internal Medicine, Oncology and Hematology, Robert-Bosch-Hospital, Auerbachstr. 110, Stuttgart 70376, Germany
| | - H Horn
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Hospital, Auerbachstr. 110, Stuttgart 70376, Germany
| | - W E Aulitzky
- Second Department of Internal Medicine, Oncology and Hematology, Robert-Bosch-Hospital, Auerbachstr. 110, Stuttgart 70376, Germany
| | - H van der Kuip
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Auerbachstr. 112, Stuttgart 70376, Germany
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He BJ, Nolte G, Nagata K, Takano D, Yamazaki T, Fujimaki Y, Maeda T, Satoh Y, Heckers S, George MS, Lopes da Silva F, de Munck JC, Van Houdt PJ, Verdaasdonk RM, Ossenblok P, Mullinger K, Bowtell R, Bagshaw AP, Keeser D, Karch S, Segmiller F, Hantschk I, Berman A, Padberg F, Pogarell O, Scharnowski F, Karch S, Hümmer S, Keeser D, Paolini M, Kirsch V, Koller G, Rauchmann B, Kupka M, Blautzik J, Pogarell O, Razavi N, Jann K, Koenig T, Kottlow M, Hauf M, Strik W, Dierks T, Gotman J, Vulliemoz S, Lu Y, Zhang H, Yang L, Worrell G, He B, Gruber O, Piguet C, Hubl D, Homan P, Kindler J, Dierks T, Kim K, Steinhoff U, Wakai R, Koenig T, Kottlow M, Melie-García L, Mucci A, Volpe U, Prinster A, Salvatore M, Galderisi S, Linden DEJ, Brandeis D, Schroeder CE, Kayser C, Panzeri S, Kleinschmidt A, Ritter P, Walther S, Haueisen J, Lau S, Flemming L, Sonntag H, Maess B, Knösche TR, Lanfer B, Dannhauer M, Wolters CH, Stenroos M, Haueisen J, Wolters C, Aydin U, Lanfer B, Lew S, Lucka F, Ruthotto L, Vorwerk J, Wagner S, Ramon C, Guan C, Ang KK, Chua SG, Kuah WK, Phua KS, Chew E, Zhou H, Chuang KH, Ang BT, Wang C, Zhang H, Yang H, Chin ZY, Yu H, Pan Y, Collins L, Mainsah B, Colwell K, Morton K, Ryan D, Sellers E, Caves K, Throckmorton S, Kübler A, Holz EM, Zickler C, Sellers E, Ryan D, Brown K, Colwell K, Mainsah B, Caves K, Throckmorton S, Collins L, Wennberg R, Ahlfors SP, Grova C, Chowdhury R, Hedrich T, Heers M, Zelmann R, Hall JA, Lina JM, Kobayashi E, Oostendorp T, van Dam P, Oosterhof P, Linnenbank A, Coronel R, van Dessel P, de Bakker J, Rossion B, Jacques C, Witthoft N, Weiner KS, Foster BL, Miller KJ, Hermes D, Parvizi J, Grill-Spector K, Recanzone GH, Murray MM, Haynes JD, Richiardi J, Greicius M, De Lucia M, Müller KR, Formisano E, Smieskova R, Schmidt A, Bendfeldt K, Walter A, Riecher-Rössler A, Borgwardt S, Fusar-Poli P, Eliez S, Schmidt A, Sekihara K, Nagarajan SS, Schoffelen JM, Guggisberg AG, Nolte G, Balazs S, Kermanshahi K, Kiesenhofer W, Binder H, Rattay F, Antal A, Chaieb L, Paulus W, Bodis-Wollner I, Maurer K, Fein G, Camchong J, Johnstone J, Cardenas-Nicolson V, Fiederer LDJ, Lucka F, Yang S, Vorwerk J, Dümpelmann M, Cosandier-Rimélé D, Schulze-Bonhage A, Aertsen A, Speck O, Wolters CH, Ball T, Fuchs M, Wagner M, Kastner J, Tech R, Dinh C, Haueisen J, Baumgarten D, Hämäläinen MS, Lau S, Vogrin SJ, D'Souza W, Haueisen J, Cook MJ, Custo A, Van De Ville D, Vulliemoz S, Grouiller F, Michel CM, Malmivuo J, Aydin U, Vorwerk J, Küpper P, Heers M, Kugel H, Wellmer J, Kellinghaus C, Scherg M, Rampp S, Wolters C, Storti SF, Boscolo Galazzo I, Del Felice A, Pizzini FB, Arcaro C, Formaggio E, Mai R, Manganotti P, Koessler L, Vignal J, Cecchin T, Colnat-Coulbois S, Vespignani H, Ramantani G, Maillard L, Rektor I, Kuba R, Brázdil M, Chrastina J, Rektorova I, van Mierlo P, Carrette E, Strobbe G, Montes-Restrepo V, Vonck K, Vandenberghe S, Ahmed B, Brodely C, Carlson C, Kuzniecky R, Devinsky O, French J, Thesen T, Bénis D, David O, Lachaux JP, Seigneuret E, Krack P, Fraix V, Chabardès S, Bastin J, Jann K, Gee D, Kilroy E, Cannon T, Wang DJ, Hale JR, Mayhew SD, Przezdzik I, Arvanitis TN, Bagshaw AP, Plomp G, Quairiaux C, Astolfi L, Michel CM, Mayhew SD, Mullinger KJ, Bagshaw AP, Bowtell R, Francis ST, Schouten AC, Campfens SF, van der Kooij H, Koles Z, Lind J, Flor-Henry P, Wirth M, Haase CM, Villeneuve S, Vogel J, Jagust WJ, Kambeitz-Ilankovic L, Simon-Vermot L, Gesierich B, Duering M, Ewers M, Rektorova I, Krajcovicova L, Marecek R, Mikl M, Bracht T, Horn H, Strik W, Federspiel A, Schnell S, Höfle O, Stegmayer K, Wiest R, Dierks T, Müller TJ, Walther S, Surmeli T, Ertem A, Eralp E, Kos IH, Skrandies W, Flüggen S, Klein A, Britz J, Díaz Hernàndez L, Ro T, Michel CM, Lenartowicz A, Lau E, Rodriguez C, Cohen MS, Loo SK, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Giannoudas I, La Porta P, Verardo AR, Niolu C, Fernandez I, Siracusano A, Flor-Henry P, Lind J, Koles Z, Bollmann S, Ghisleni C, O'Gorman R, Poil SS, Klaver P, Michels L, Martin E, Ball J, Eich-Höchli D, Brandeis D, Salisbury DF, Murphy TK, Butera CD, Mathalon DH, Fryer SL, Kiehl KA, Calhoun VC, Pearlson GD, Roach BJ, Ford JM, McGlashan TH, Woods SW, Volpe U, Merlotti E, Vignapiano A, Montefusco V, Plescia GM, Gallo O, Romano P, Mucci A, Galderisi S, Mingoia G, Langbein K, Dietzek M, Wagner G, Smesny, Scherpiet S, Maitra R, Gaser C, Sauer H, Nenadic I, Gonzalez Andino S, Grave de Peralta Menendez R, Grave de Peralta Menendez R, Sanchez Vives M, Rebollo B, Gonzalez Andino S, Frølich L, Andersen TS, Mørup M, Belfiore P, Gargiulo P, Ramon C, Vanhatalo S, Cho JH, Vorwerk J, Wolters CH, Knösche TR, Watanabe T, Kawabata Y, Ukegawa D, Kawabata S, Adachi Y, Sekihara K, Sekihara K, Nagarajan SS, Wagner S, Aydin U, Vorwerk J, Herrmann C, Burger M, Wolters C, Lucka F, Aydin U, Vorwerk J, Burger M, Wolters C, Bauer M, Trahms L, Sander T, Faber PL, Lehmann D, Gianotti LRR, Pascual-Marqui RD, Milz P, Kochi K, Kaneko S, Yamashita S, Yana K, Kalogianni K, Vardy AN, Schouten AC, van der Helm FCT, Sorrentino A, Luria G, Aramini R, Hunold A, Funke M, Eichardt R, Haueisen J, Gómez-Aguilar F, Vázquez-Olvera S, Cordova-Fraga T, Castro-López J, Hernández-Gonzalez MA, Solorio-Meza S, Sosa-Aquino M, Bernal-Alvarado JJ, Vargas-Luna M, Vorwerk J, Magyari L, Ludewig J, Oostenveld R, Wolters CH, Vorwerk J, Engwer C, Ludewig J, Wolters C, Sato K, Nishibe T, Furuya M, Yamashiro K, Yana K, Ono T, Puthanmadam Subramaniyam N, Hyttinen J, Lau S, Güllmar D, Flemming L, Haueisen J, Sonntag H, Vorwerk J, Wolters CH, Grasedyck L, Haueisen J, Maeß B, Freitag S, Graichen U, Fiedler P, Strohmeier D, Haueisen J, Stenroos M, Hauk O, Grigutsch M, Felber M, Maess B, Herrmann B, Strobbe G, van Mierlo P, Vandenberghe S, Strobbe G, Cárdenas-Peña D, Montes-Restrepo V, van Mierlo P, Castellanos-Dominguez G, Vandenberghe S, Lanfer B, Paul-Jordanov I, Scherg M, Wolters CH, Ito Y, Sato D, Kamada K, Kobayashi T, Dalal SS, Rampp S, Willomitzer F, Arold O, Fouladi-Movahed S, Häusler G, Stefan H, Ettl S, Zhang S, Zhang Y, Li H, Kong X, Montes-Restrepo V, Strobbe G, van Mierlo P, Vandenberghe S, Wong DDE, Bidet-Caulet A, Knight RT, Crone NE, Dalal SS, Birot G, Spinelli L, Vulliémoz S, Seeck M, Michel CM, Emory H, Wells C, Mizrahi N, Vogrin SJ, Lau S, Cook MJ, Karahanoglu FI, Grouiller F, Caballero-Gaudes C, Seeck M, Vulliemoz S, Van De Ville D, Spinelli L, Megevand P, Genetti M, Schaller K, Michel C, Vulliemoz S, Seeck M, Genetti M, Tyrand R, Grouiller F, Vulliemoz S, Spinelli L, Seeck M, Schaller K, Michel CM, Grouiller F, Heinzer S, Delattre B, Lazeyras F, Spinelli L, Pittau F, Seeck M, Ratib O, Vargas M, Garibotto V, Vulliemoz S, Vogrin SJ, Bailey CA, Kean M, Warren AE, Davidson A, Seal M, Harvey AS, Archer JS, Papadopoulou M, Leite M, van Mierlo P, Vonck K, Boon P, Friston K, Marinazzo D, Ramon C, Holmes M, Koessler L, Rikir E, Gavaret M, Bartolomei F, Vignal JP, Vespignani H, Maillard L, Centeno M, Perani S, Pier K, Lemieux L, Clayden J, Clark C, Pressler R, Cross H, Carmichael DW, Spring A, Bessemer R, Pittman D, Aghakhani Y, Federico P, Pittau F, Grouiller F, Vulliémoz S, Gotman J, Badier JM, Bénar CG, Bartolomei F, Cruto C, Chauvel P, Gavaret M, Brodbeck V, van Leeuwen T, Tagliazzuchi E, Melloni L, Laufs H, Griskova-Bulanova I, Dapsys K, Klein C, Hänggi J, Jäncke L, Ehinger BV, Fischer P, Gert AL, Kaufhold L, Weber F, Marchante Fernandez M, Pipa G, König P, Sekihara K, Hiyama E, Koga R, Iannilli E, Michel CM, Bartmuss AL, Gupta N, Hummel T, Boecker R, Holz N, Buchmann AF, Blomeyer D, Plichta MM, Wolf I, Baumeister S, Meyer-Lindenberg A, Banaschewski T, Brandeis D, Laucht M, Natahara S, Ueno M, Kobayashi T, Kottlow M, Bänninger A, Koenig T, Schwab S, Koenig T, Federspiel A, Dierks T, Jann K, Natsukawa H, Kobayashi T, Tüshaus L, Koenig T, Kottlow M, Achermann P, Wilson RS, Mayhew SD, Assecondi S, Arvanitis TN, Bagshaw AP, Darque A, Rihs TA, Grouiller F, Lazeyras F, Ha-Vinh Leuchter R, Caballero C, Michel CM, Hüppi PS, Hauser TU, Hunt LT, Iannaccone R, Stämpfli P, Brandeis D, Dolan RJ, Walitza S, Brem S, Graichen U, Eichardt R, Fiedler P, Strohmeier D, Freitag S, Zanow F, Haueisen J, Lordier L, Grouiller F, Van de Ville D, Sancho Rossignol A, Cordero I, Lazeyras F, Ansermet F, Hüppi P, Schläpfer A, Rubia K, Brandeis D, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Giannoudas I, Verardo AR, La Porta P, Niolu C, Fernandez I, Siracusano A, Tamura K, Karube C, Mizuba T, Matsufuji M, Takashima S, Iramina K, Assecondi S, Ostwald D, Bagshaw AP, Marecek R, Brazdil M, Lamos M, Slavícek T, Marecek R, Jan J, Meier NM, Perrig W, Koenig T, Minami T, Noritake Y, Nakauchi S, Azuma K, Minami T, Nakauchi S, Rodriguez C, Lenartowicz A, Cohen MS, Rodriguez C, Lenartowicz A, Cohen MS, Iramina K, Kinoshita H, Tamura K, Karube C, Kaneko M, Ide J, Noguchi Y, Cohen MS, Douglas PK, Rodriguez CM, Xia HJ, Zimmerman EM, Konopka CJ, Epstein PS, Konopka LM, Giezendanner S, Fisler M, Soravia L, Andreotti J, Wiest R, Dierks T, Federspiel A, Razavi N, Federspiel A, Dierks T, Hauf M, Jann K, Kamada K, Sato D, Ito Y, Okano K, Mizutani N, Kobayashi T, Thelen A, Murray M, Pastena L, Formaggio E, Storti SF, Faralli F, Melucci M, Gagliardi R, Ricciardi L, Ruffino G, Coito A, Macku P, Tyrand R, Astolfi L, He B, Wiest R, Seeck M, Michel C, Plomp G, Vulliemoz S, Fischmeister FPS, Glaser J, Schöpf V, Bauer H, Beisteiner R, Deligianni F, Centeno M, Carmichael DW, Clayden J, Mingoia G, Langbein K, Dietzek M, Wagner G, Smesny S, Scherpiet S, Maitra R, Gaser C, Sauer H, Nenadic I, Dürschmid S, Zaehle T, Pannek H, Chang HF, Voges J, Rieger J, Knight RT, Heinze HJ, Hinrichs H, Tsatsishvili V, Cong F, Puoliväli T, Alluri V, Toiviainen P, Nandi AK, Brattico E, Ristaniemi T, Grieder M, Crinelli RM, Jann K, Federspiel A, Wirth M, Koenig T, Stein M, Wahlund LO, Dierks T, Atsumori H, Yamaguchi R, Okano Y, Sato H, Funane T, Sakamoto K, Kiguchi M, Tränkner A, Schindler S, Schmidt F, Strauß M, Trampel R, Hegerl U, Turner R, Geyer S, Schönknecht P, Kebets V, van Assche M, Goldstein R, van der Meulen M, Vuilleumier P, Richiardi J, Van De Ville D, Assal F, Wozniak-Kwasniewska A, Szekely D, Harquel S, Bougerol T, David O, Bracht T, Jones DK, Horn H, Müller TJ, Walther S, Sos P, Klirova M, Novak T, Brunovsky M, Horacek J, Bares M, Hoschl C C, Fellhauer I, Zöllner FG, Schröder J, Kong L, Essig M, Schad LR, Arrubla J, Neuner I, Hahn D, Boers F, Shah NJ, Neuner I, Arrubla J, Hahn D, Boers F, Jon Shah N, Suriya Prakash M, Sharma R, Kawaguchi H, Kobayashi T, Fiedler P, Griebel S, Biller S, Fonseca C, Vaz F, Zentner L, Zanow F, Haueisen J, Rochas V, Rihs T, Thut G, Rosenberg N, Landis T, Michel C, Moliadze V, Schmanke T, Lyzhko E, Bassüner S, Freitag C, Siniatchkin M, Thézé R, Guggisberg AG, Nahum L, Schnider A, Meier L, Friedrich H, Jann K, Landis B, Wiest R, Federspiel A, Strik W, Dierks T, Witte M, Kober SE, Neuper C, Wood G, König R, Matysiak A, Kordecki W, Sieluzycki C, Zacharias N, Heil P, Wyss C, Boers F, Arrubla J, Dammers J, Kawohl W, Neuner I, Shah NJ, Braboszcz C, Cahn RB, Levy J, Fernandez M, Delorme A, Rosas-Martinez L, Milne E, Zheng Y, Urakami Y, Kawamura K, Washizawa Y, Hiyoshi K, Cichocki A, Giroud N, Dellwo V, Meyer M, Rufener KS, Liem F, Dellwo V, Meyer M, Jones-Rounds JD, Raizada R, Staljanssens W, Strobbe G, van Mierlo P, Van Holen R, Vandenberghe S, Pefkou M, Becker R, Michel C, Hervais-Adelman A, He W, Brock J, Johnson B, Ohla K, Hitz K, Heekeren K, Obermann C, Huber T, Juckel G, Kawohl W, Gabriel D, Comte A, Henriques J, Magnin E, Grigoryeva L, Ortega JP, Haffen E, Moulin T, Pazart L, Aubry R, Kukleta M, Baris Turak B, Louvel J, Crespo-Garcia M, Cantero JL, Atienza M, Connell S, Kilborn K, Damborská A, Brázdil M, Rektor I, Kukleta M, Koberda JL, Bienkiewicz A, Koberda I, Koberda P, Moses A, Tomescu M, Rihs T, Britz J, Custo A, Grouiller F, Schneider M, Debbané M, Eliez S, Michel C, Wang GY, Kydd R, Wouldes TA, Jensen M, Russell BR, Dissanayaka N, Au T, Angwin A, O'Sullivan J, Byrne G, Silburn P, Marsh R, Mellic G, Copland D, Bänninger A, Kottlow M, Díaz Hernàndez L, Koenig T, Díaz Hernàndez L, Bänninger A, Koenig T, Hauser TU, Iannaccone R, Mathys C, Ball J, Drechsler R, Brandeis D, Walitza S, Brem S, Boeijinga PH, Pang EW, Valica T, Macdonald MJ, Oh A, Lerch JP, Anagnostou E, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Verardo AR, Giannoudas I, La Porta P, Niolu C, Fernandez I, Siracusano A, Shimada T, Matsuda Y, Monkawa A, Monkawa T, Hashimoto R, Watanabe K, Kawasaki Y, Matsuda Y, Shimada T, Monkawa T, Monkawa A, Watanabe K, Kawasaki Y, Stegmayer K, Horn H, Federspiel A, Razavi N, Bracht T, Laimböck K, Strik W, Dierks T, Wiest R, Müller TJ, Walther S, Koorenhof LJ, Swithenby SJ, Martins-Mourao A, Rihs TA, Tomescu M, Song KW, Custo A, Knebel JF, Murray M, Eliez S, Michel CM, Volpe U, Merlotti E, Vignapiano A, Montefusco V, Plescia GM, Gallo O, Romano P, Mucci A, Galderisi S, Laimboeck K, Jann K, Walther S, Federspiel A, Wiest R, Strik W, Horn H. Abstracts of Presentations at the International Conference on Basic and Clinical Multimodal Imaging (BaCI), a Joint Conference of the International Society for Neuroimaging in Psychiatry (ISNIP), the International Society for Functional Source Imaging (ISFSI), the International Society for Bioelectromagnetism (ISBEM), the International Society for Brain Electromagnetic Topography (ISBET), and the EEG and Clinical Neuroscience Society (ECNS), in Geneva, Switzerland, September 5-8, 2013. Clin EEG Neurosci 2013; 44:1550059413507209. [PMID: 24368763 DOI: 10.1177/1550059413507209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- B J He
- National Institutes of Health, Bethesda, MD, USA
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Rocktäschel T, Klarmann C, Helmreich B, Ochoa J, Boisson P, Sørensen KH, Horn H. Comparison of two different anaerobic feeding strategies to establish a stable aerobic granulated sludge bed. Water Res 2013; 47:6423-6431. [PMID: 24103394 DOI: 10.1016/j.watres.2013.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 06/02/2023]
Abstract
Two different anaerobic feeding strategies were compared to optimize the development and performance of aerobic granules. A stable aerobic granulation of activated sludge was achieved with an anaerobic plug flow operation (PI) and a fast influent step followed by an anaerobic mixing phase (PII). Two lab scale sequencing batch reactors (SBRs) were operated to test the different operation modes. PI with plug flow and a reactor H/D (height/diameter) ratio of 9 achieved a biomass concentration of 20 g(TSS)/L and an effluent TSS concentration of 0.10 g(TSS)/L. PII with the mixed anaerobic phase directly after feeding and a reactor H/D ratio of 2 achieved a biomass concentration of 9 g(TSS)/L and an effluent quality of 0.05 g(TSS)/L. Furthermore, it is shown that the plug flow regime during anaerobic feeding together with the lower H/D ratio of 2 led to channeling effects, which resulted in lower storage of organic carbon and a general destabilization of the granulation process. Compared to the plug flow regime (PI), the anaerobic mixing (PII) provided lower substrate gradients within the biofilm. However, these disadvantages could be compensated by higher mass transfer coefficients in PII (k(L) = 0.3 m/d for PI; k(L) = 86 m/d for PII) during the anaerobic phase.
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Affiliation(s)
- T Rocktäschel
- Technische Universität München, Chair of Urban Water Systems Engineering, Am Coulombwall, 85748 Garching, Germany
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Walther S, Ramseyer F, Horn H, Strik W, Tschacher W. Disorganization and movement patterns in schizophrenia. Pharmacopsychiatry 2013. [DOI: 10.1055/s-0033-1353349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Walther S, Moggi F, Horn H, Moskvitin K, Maier N, Abderhalden C, Strik W, Müller TJ. Rapid tranquilization of severely agitated patients with schizophrenia spectrum disorders: a naturalistic, rater-blinded, randomized controlled study with oral haloperidol, risperidone, and olanzapine. Pharmacopsychiatry 2013. [DOI: 10.1055/s-0033-1353338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Würtz SØ, Schrohl AS, Damsgaard B, Rømer MU, Belling KC, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brünner N, Olsen JV, Stenvang J. TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. J Proteome Res 2013; 12:4136-51. [PMID: 23909892 DOI: 10.1021/pr400457u] [Citation(s) in RCA: 28] [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: 01/13/2023]
Abstract
Tissue inhibitor of metalloproteinase 1 (TIMP-1) is a protein with a potential biological role in drug resistance. To elucidate the unknown molecular mechanisms underlying the association between high TIMP-1 levels and increased chemotherapy resistance, we employed SILAC-based quantitative mass spectrometry to analyze global proteome and phosphoproteome differences of MCF-7 breast cancer cells expressing high or low levels of TIMP-1. In TIMP-1 high expressing cells, 312 proteins and 452 phosphorylation sites were up-regulated. Among these were the cancer drug targets topoisomerase 1, 2A, and 2B, which may explain the resistance phenotype to topoisomerase inhibitors that was observed in cells with high TIMP-1 levels. Pathway analysis showed an enrichment of proteins from functional categories such as apoptosis, cell cycle, DNA repair, transcription factors, drug targets and proteins associated with drug resistance or sensitivity, and drug transportation. The NetworKIN algorithm predicted the protein kinases CK2a, CDK1, PLK1, and ATM as likely candidates involved in the hyperphosphorylation of the topoisomerases. Up-regulation of protein and/or phosphorylation levels of topoisomerases in TIMP-1 high expressing cells may be part of the mechanisms by which TIMP-1 confers resistance to treatment with the widely used topoisomerase inhibitors in breast and colorectal cancer.
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Affiliation(s)
- Omid Hekmat
- Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Dyrlægevej 88, 1., 1870 Frederiksberg C, Denmark
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Lundby A, Andersen MN, Steffensen AB, Horn H, Kelstrup CD, Francavilla C, Jensen LJ, Schmitt N, Thomsen MB, Olsen JV. In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling. Sci Signal 2013; 6:rs11. [PMID: 23737553 DOI: 10.1126/scisignal.2003506] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
β-Blockers are widely used to prevent cardiac arrhythmias and to treat hypertension by inhibiting β-adrenergic receptors (βARs) and thus decreasing contractility and heart rate. βARs initiate phosphorylation-dependent signaling cascades, but only a small number of the target proteins are known. We used quantitative in vivo phosphoproteomics to identify 670 site-specific phosphorylation changes in murine hearts in response to acute treatment with specific βAR agonists. The residues adjacent to the regulated phosphorylation sites exhibited a sequence-specific preference (R-X-X-pS/T), and integrative analysis of sequence motifs and interaction networks suggested that the kinases AMPK (adenosine 5'-monophosphate-activated protein kinase), Akt, and mTOR (mammalian target of rapamycin) mediate βAR signaling, in addition to the well-established pathways mediated by PKA (cyclic adenosine monophosphate-dependent protein kinase) and CaMKII (calcium/calmodulin-dependent protein kinase type II). We found specific regulation of phosphorylation sites on six ion channels and transporters that mediate increased ion fluxes at higher heart rates, and we showed that phosphorylation of one of these, Ser(92) of the potassium channel KV7.1, increased current amplitude. Our data set represents a quantitative analysis of phosphorylated proteins regulated in vivo upon stimulation of seven-transmembrane receptors, and our findings reveal previously unknown phosphorylation sites that regulate myocardial contractility, suggesting new potential targets for the treatment of heart disease and hypertension.
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Affiliation(s)
- Alicia Lundby
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
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Abstract
Grey zone lymphomas are lymphatic tumors that cannot be assigned to a defined lymphoma entity due to morphological, clinical or genetic reasons. As a defining criterion they present with features of two overlapping entities or features that are intermediate. Such lymphomas may represent a grey zone in the differentiation between indolent and aggressive lymphomas. Often they may show morphological features of one entity but be more related to another entity with respect to the immunophenotype and/or genetic constitution, such as lymphomas in the grey zone between primary mediastinal large B-cell lymphoma and primary nodal diffuse large B-cell lymphoma. The B-cell lymphoma, unclassified, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma has recently been recognized as a provisional category in the updated WHO 2008 classification of malignant lymphomas. This corresponds to a practical lymphoma category that obviously contains several entities with a Burkitt-like appearance and aggressive clinical behavior. Genetically, tumors in this category are frequently characterized by an atypical MYC translocation and complex karyotypic alterations. As yet, no adequate therapy concept exists.
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Affiliation(s)
- M M Ott
- Pathologisches Institut, Caritas-Krankenhaus, Bad Mergentheim, Deutschland
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Liu S, Horn H, Müller E. A systematic insight into a single-stage deammonification process operated in granular sludge reactor with high-loaded reject-water: characterization and quantification of microbiological community. J Appl Microbiol 2012; 114:339-51. [DOI: 10.1111/jam.12042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 09/04/2012] [Accepted: 09/11/2012] [Indexed: 11/28/2022]
Affiliation(s)
- S.T. Liu
- Institute of Water Quality Control; Technische Universität München; Garching Germany
- Department of Environmental Engineering; Peking University; The Key Laboratory of Water and Sediment Sciences; Ministry of Education; Beijing China
| | - H. Horn
- Karlsruhe Institute of Technology (KIT); Engler-Bunte-Institute; Water Chemistry and Water Technology; Karlsruhe Germany
| | - E. Müller
- Institute of Water Quality Control; Technische Universität München; Garching Germany
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Lenze D, Leoncini L, Hummel M, Volinia S, Liu CG, Amato T, De Falco G, Githanga J, Horn H, Nyagol J, Ott G, Palatini J, Pfreundschuh M, Rogena E, Rosenwald A, Siebert R, Croce CM, Stein H. The different epidemiologic subtypes of Burkitt lymphoma share a homogenous micro RNA profile distinct from diffuse large B-cell lymphoma. Leukemia 2011; 25:1869-1876. [PMID: 21701491 PMCID: PMC3902789 DOI: 10.1038/leu.2011.156] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/06/2011] [Accepted: 05/03/2011] [Indexed: 12/19/2022]
Abstract
Sporadic Burkitt lymphoma (sBL) can be delineated from diffuse large B-cell lymphoma (DLBCL) by a very homogeneous mRNA expression signature. However, it remained unclear whether all three BL variants-sBL, endemic BL (eBL) and human immunodeficiency virus-associated BL (HIV-BL)-represent a uniform biological entity despite their differences in geographical occurrence, association with immunodeficiency and/or incidence of Epstein-Barr virus (EBV) infection. To address this issue, we generated micro RNA (miRNA) profiles from 18 eBL, 31 sBL and 15 HIV-BL cases. In addition, we analyzed the miRNA expression of 86 DLBCL to determine whether miRNA profiles recapitulate the molecular differences between BL and DLBCL evidenced by mRNA profiling. A signature of 38 miRNAs containing MYC regulated and nuclear factor-kB pathway-associated miRNAs was obtained that differentiated BL from DLBCL. The miRNA profiles of sBL and eBL displayed only six differentially expressed miRNAs, whereas HIV and EBV infection had no impact on the miRNA profile of BL. In conclusion, miRNA profiling confirms that BL and DLBCL represent distinct lymphoma categories and demonstrates that the three BL variants are representatives of the same biological entity with only marginal miRNA expression differences between eBL and sBL.
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Affiliation(s)
- D Lenze
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - L Leoncini
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
| | - M Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - S Volinia
- Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - CG Liu
- Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - T Amato
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
| | - G De Falco
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
| | - J Githanga
- Department of Human Pathology, University of Nairobi, Nairobi, Kenya
| | - H Horn
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Würzburg, Stuttgart, Germany
| | - J Nyagol
- Department of Human Pathology, University of Nairobi, Nairobi, Kenya
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Hospital, Stuttgart, Germany
| | - J Palatini
- Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | | | - E Rogena
- Department of Human Pathology, University of Nairobi, Nairobi, Kenya
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany, Campus Kiel, Kiel, Germany
| | - R Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - CM Croce
- Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - H Stein
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
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48
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Abstract
Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated with diseases are in linkage disequilibrium (LD) with a gene of interest? Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not in LD are in different blocks. By projecting SNPs and genes onto LD blocks, the DistiLD database aims to increase usage of existing GWAS results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database is available at http://distild.jensenlab.org/.
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Affiliation(s)
- Albert Pallejà
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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49
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Koos B, Horn H, Schaupp E, Axmann D, Berneburg M. Lip and tongue movements during phonetic sequences: analysis and definition of normal values. Eur J Orthod 2011; 35:51-8. [DOI: 10.1093/ejo/cjr082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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50
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Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ, Choudhary C. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Sci Signal 2011; 4:ra48. [PMID: 21791702 DOI: 10.1126/scisignal.2001902] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Posttranslational modification of proteins by acetylation and phosphorylation regulates most cellular processes in living organisms. Surprisingly, the evolutionary conservation of phosphorylated serine and threonine residues is only marginally higher than that of unmodified serines and threonines. With high-resolution mass spectrometry, we identified 1981 lysine acetylation sites in the proteome of Drosophila melanogaster. We used data sets of experimentally identified acetylation and phosphorylation sites in Drosophila and humans to analyze the evolutionary conservation of these modification sites between flies and humans. Site-level conservation analysis revealed that acetylation sites are highly conserved, significantly more so than phosphorylation sites. Furthermore, comparison of lysine conservation in Drosophila and humans with that in nematodes and zebrafish revealed that acetylated lysines were significantly more conserved than were nonacetylated lysines. Bioinformatics analysis using Gene Ontology terms suggested that the proteins with conserved acetylation control cellular processes such as protein translation, protein folding, DNA packaging, and mitochondrial metabolism. We found that acetylation of ubiquitin-conjugating E2 enzymes was evolutionarily conserved, and mutation of a conserved acetylation site impaired the function of the human E2 enzyme UBE2D3. This systems-level analysis of comparative posttranslational modification showed that acetylation is an anciently conserved modification and suggests that phosphorylation sites may have evolved faster than acetylation sites.
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Affiliation(s)
- Brian T Weinert
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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