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Kumar S, Hausen J, Sivalingam S, Humbatova A, Buness A, Frank J, Ralser DJ, Betz RC. Altered Notch signalling in Dowling-Degos disease: a transcriptomic insight into disease pathogenesis. Br J Dermatol 2023; 189:772-774. [PMID: 37625796 DOI: 10.1093/bjd/ljad306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 08/27/2023]
Abstract
Dowling-Degos disease (DDD) is a rare autosomal-dominant hyperpigmentation disorder caused by mutations in KRT5, POFUT1, POGLUT1 and PSENEN. Our results suggest that dysfunctional Notch signalling in melanocytes plays a key role in DDD pathogenesis, and that altered biogenesis and intracellular trafficking of melanosomes, receptor tyrosine kinase signalling and oestrogen signalling receptor-mediated signalling may represent downstream molecular mechanisms through which decreased Notch signalling leads to hyperpigmentation in DDD. Furthermore, a common downstream pathomechanism for both POGLUT1 and PSENEN mutation carriers can be assumed.
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Affiliation(s)
- Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Aytaj Humbatova
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn Germany
| | - Jorge Frank
- Department of Dermatology, Venereology and Allergology, University Medical Center Göttingen, Göttingen, Germany
| | - Damian J Ralser
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
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2
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Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E. Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Mol Genet Genomic Med 2023; 11:e2109. [PMID: 36468602 PMCID: PMC10009911 DOI: 10.1002/mgg3.2109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Sarah L Mehrem
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ariane C Fechtner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Ruth Raff
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.,Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Khalid Aldhorae
- Department of Orthodontics, College of Dentistry, Thamar University, Thamar, Yemen.,Department of Orthodontics, College of Dentistry, University of Ibn al-Nafis for Medical Sciences, Sanaa, Yemen
| | - Bert Braumann
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Teresa Kruse
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | | | - Gerrit Spanier
- Department of Cranio-Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Erlangen-Nürnberg, Erlangen, Germany.,Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,University Hospital Cologne, Cologne, Germany
| | - Tim Becker
- Institute of Community Medicine, University of Greifswald, Greifswald, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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3
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Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Hum Mutat 2021; 42:1066-1078. [PMID: 34004033 DOI: 10.1002/humu.24219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
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Affiliation(s)
- Frederic Thieme
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nigel L Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nina Ishorst
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonas Hausen
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Antony D Adamson
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Angelika Biedermann
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Hanna K Zieger
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Carlo Maj
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Andreas Buness
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany.,Department of Orthodontics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Bert Braumann
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Khalid Aldhorae
- Department of Orthodontics, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey, Mexico
| | - Peter M Krawitz
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
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4
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Volz SN, Hausen J, Nachev M, Ottermanns R, Schiwy S, Hollert H. Short exposure to cadmium disrupts the olfactory system of zebrafish (Danio rerio) - Relating altered gene expression in the olfactory organ to behavioral deficits. Aquat Toxicol 2020; 226:105555. [PMID: 32645607 DOI: 10.1016/j.aquatox.2020.105555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/22/2019] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Fish strongly rely on olfaction as a variety of essential behaviors such as foraging and predator avoidance are mediated by the olfactory system. Cadmium (Cd) is known to impair olfaction and accumulate in the olfactory epithelium (OE) and bulb (OB) of fishes. In the present study, the acute toxicity of Cd on olfaction in zebrafish (Danio rerio) was characterized on the molecular and behavioral level. To this end, quantitative real-time PCR was performed in order to analyze the expression of selected genes in both the OE and OB. Moreover, the response of zebrafish to an alarm cue was investigated. Following 24 h of exposure to Cd, the expression of genes associated with olfactory sensory neurons was reduced in the OE. Furthermore, the antioxidant genes peroxiredoxin 1 (prdx1) and heme oxygenase 1 (hmox1), as well as the metallothionein 2 gene (mt2) were upregulated in the OE, whereas hmox1 and the stress-inducible heat shock protein 70 gene (hsp70) were upregulated in the OB upon exposure to Cd. Following stimulation with a conspecific skin extract, zebrafish displayed a considerable disruption of the antipredator behavior with increasing Cd concentration. Taken together, Cd impaired olfaction in zebrafish, thereby disrupting the antipredator response, which is crucial for the survival of individuals. Cellular stress followed by disruption of olfactory sensory neurons may have contributed to the observed behavioral deficits.
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Affiliation(s)
- Sina N Volz
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Jonas Hausen
- Core Unit for Bioinformatics Data Analysis, University of Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Milen Nachev
- Aquatic Ecology and Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany.
| | - Richard Ottermanns
- Chair of Environmental Biology and Chemodynamics, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Sabrina Schiwy
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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5
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Volz SN, Hausen J, Smith K, Ottermanns R, Schaeffer A, Schiwy S, Hollert H. Do you smell the danger? Effects of three commonly used pesticides on the olfactory-mediated antipredator response of zebrafish (Danio rerio). Chemosphere 2020; 241:124963. [PMID: 31604193 DOI: 10.1016/j.chemosphere.2019.124963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Fish are warned about the presence of predators via an alarm cue released from the skin of injured conspecifics. The detection of this odor inherently initiates an antipredator response, which increases the chance of survival for the individual. In the present study, we assessed the effect of three commonly used pesticides on the antipredator response of zebrafish (Danio rerio). For this, we analyzed the behavioral response of zebrafish to a conspecific skin extract following 24 h of exposure to the respective contaminants. Results demonstrate that fish exposed to 20 μg/L of the organophosphate insecticide chlorpyrifos significantly reduced bottom-dwelling and freezing behavior, suggesting an impairment of the antipredator response. For the urea-herbicide linuron and the pyrethroid insecticide permethrin, no statistically significant effects could be detected. However, linuron-exposed fish appeared to respond in an altered manner to the skin extract; some individuals failed to perform the inherent behaviors such as erratic movements and instead merely increased their velocity. Furthermore, we determined whether zebrafish would avoid the pesticides in a choice maze. While fish avoided permethrin, they behaved indifferently to chlorpyrifos and linuron. The study demonstrates that pesticides may alter the olfactory-mediated antipredator response of zebrafish in distinct ways, revealing that particularly fish exposed to chlorpyrifos may be more prone to predation.
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Affiliation(s)
- Sina N Volz
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Jonas Hausen
- Core Unit for Bioinformatics Data Analysis, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Kilian Smith
- Chair of Environmental Biology and Chemodynamics, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Richard Ottermanns
- Chair of Environmental Biology and Chemodynamics, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Andreas Schaeffer
- Chair of Environmental Biology and Chemodynamics, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Sabrina Schiwy
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.
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6
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Hausen J, Otte JC, Legradi J, Yang L, Strähle U, Fenske M, Hecker M, Tang S, Hammers-Wirtz M, Hollert H, Keiter SH, Ottermanns R. Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos. Environ Sci Pollut Res Int 2018; 25:4023-4036. [PMID: 28391457 DOI: 10.1007/s11356-017-8977-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 11/25/2016] [Accepted: 04/03/2017] [Indexed: 05/10/2023]
Abstract
In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes. We analyzed the altered transcriptome to detect discriminative genes significantly regulated in reaction to the three applied contaminants. By comparison of the results of the three contaminants, we identified transcriptome signatures and biologically important pathways (using Cytoscape/ClueGO software) that react significantly to the contaminant classes. This approach increases the chance of finding genes that play an important role in contaminant class-specific pathways rather than more general processes.
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Affiliation(s)
- Jonas Hausen
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Jens C Otte
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jessica Legradi
- Environment and Health, VU Amsterdam, De Boelelaan 1087, 1081 HV, Amsterdam, the Netherlands
| | - Lixin Yang
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martina Fenske
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group for Translational Medicine and Pharmacology, Forckenbeckstraße 6, 52074, Aachen, Germany
| | - Markus Hecker
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada
| | - Monika Hammers-Wirtz
- Research Institute for Ecosystem Analysis and Assessment - gaiac, Kackertstraße 10, 52072, Aachen, Germany
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Steffen H Keiter
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Man-Technology-Environment Research Centre, Örebro University, SE-701 82, Örebro, Sweden
| | - Richard Ottermanns
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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7
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Hausen J, Scholz-Starke B, Burkhardt U, Lesch S, Rick S, Russell D, Roß-Nickoll M, Ottermanns R. Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse. Database (Oxford) 2017; 2017:4564813. [PMID: 29220469 PMCID: PMC5737075 DOI: 10.1093/database/bax080] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/06/2017] [Indexed: 11/21/2022]
Abstract
The Edaphostat web application allows interactive and dynamic analyses of soil organism data stored in the Edaphobase data warehouse. It is part of the Edaphobase web application and can be accessed by any modern browser. The tool combines data from different sources (publications, field studies and museum collections) and allows species preferences along various environmental gradients (i.e. C/N ratio and pH) and classification systems (habitat type and soil type) to be analyzed. Database URL: Edaphostat is part of the Edaphobase Web Application available at https://portal.edaphobase.org
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Affiliation(s)
- Jonas Hausen
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Björn Scholz-Starke
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulrich Burkhardt
- Senckenberg Museum of Natural History Görlitz, P.O. Box 300154, 02806 Görlitz, Germany
| | - Stephan Lesch
- Senckenberg Museum of Natural History Görlitz, P.O. Box 300154, 02806 Görlitz, Germany
| | - Sebastian Rick
- Senckenberg Museum of Natural History Görlitz, P.O. Box 300154, 02806 Görlitz, Germany
| | - David Russell
- Senckenberg Museum of Natural History Görlitz, P.O. Box 300154, 02806 Görlitz, Germany
| | - Martina Roß-Nickoll
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Richard Ottermanns
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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8
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Joel AC, Habedank A, Hausen J, Mey J. Fighting for the web: competition between female feather-legged spiders (Uloborus plumipes). ZOOLOGY 2016; 121:10-17. [PMID: 28109659 DOI: 10.1016/j.zool.2016.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 10/16/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022]
Abstract
Most spider species are solitary, and among the few social interactions among them, resource competition between females has received little attention. We discovered that females of the feather-legged spider Uloborus plumipes invade the orb webs of conspecifics and compete for webs. Following observations in the wild, intruder-defender interactions were studied in a terrarium and in controlled laboratory experiments. We found that contests for orb webs occurred spontaneously between adult females. Competitive interactions in U. plumipes were characterized by an escalation of ritualized behaviors. In 27% of the contests the winner was determined by interactions at a distance, which involved behaviors that caused vibratory signaling on the web. The remaining interactions escalated to physical contact, and in 78% of these a fight occurred between the contestants. Using multivariate logistic regression we determined the factors that predicted the outcome of the contests: (i) Web ownership did not give the defender a competitive advantage. (ii) The difference in physical size between the competing spiders was the most important predictor for the outcome of web contests. (iii) Independent of body size, the display of certain behaviors, specifically the ability to reach the hub before the contestant and the frequency of attacks, increased the probability of winning. (iv) Winning or losing a fight did not affect the chances of winning subsequent contests. The interactions reported here provide a promising approach to investigate communication in spiders and to test theoretical models of intraspecific competition.
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Affiliation(s)
- Anna-Christin Joel
- Institut für Biologie II (Zoologie), RWTH Aachen, Worringerweg 1, D-52074 Aachen, Germany
| | - Anne Habedank
- Institut für Biologie II (Zoologie), RWTH Aachen, Worringerweg 1, D-52074 Aachen, Germany
| | - Jonas Hausen
- Institut für Biologie V (Umweltforschung), RWTH Aachen, Worringerweg 3, D-52074 Aachen, Germany
| | - Jörg Mey
- Institut für Biologie II (Zoologie), RWTH Aachen, Worringerweg 1, D-52074 Aachen, Germany; Hospital Nacional de Parapléjicos, SESCAM, Finca la Peraleda s/n, 45071 Toledo, Spain.
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Hausen J, Otte JC, Strähle U, Hammers-Wirtz M, Hollert H, Keiter SH, Ottermanns R. Fold-change threshold screening: a robust algorithm to unmask hidden gene expression patterns in noisy aggregated transcriptome data. Environ Sci Pollut Res Int 2015; 22:16384-16392. [PMID: 26178833 DOI: 10.1007/s11356-015-5019-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 07/31/2014] [Accepted: 07/02/2015] [Indexed: 06/04/2023]
Abstract
Transcriptomics is often used to investigate changes in an organism's genetic response to environmental contamination. Data noise can mask the effects of contaminants making it difficult to detect responding genes. Because the number of genes which are found differentially expressed in transcriptome data is often very large, algorithms are needed to reduce the number down to a few robust discriminative genes. We present an algorithm for aggregated analysis of transcriptome data which uses multiple fold-change thresholds (threshold screening) and p values from Bayesian generalized linear model in order to assess the robustness of a gene as a potential indicator for the treatments tested. The algorithm provides a robustness indicator (ROBI) as well as a significance profile, which can be used to assess the statistical significance of a given gene for different fold-change thresholds. Using ROBI, eight discriminative genes were identified from an exemplary dataset (Danio rerio FET treated with chlorpyrifos, methylmercury, and PCB) which could be potential indicators for a given substance. Significance profiles uncovered genetic effects and revealed appropriate fold-change thresholds for single genes or gene clusters. Fold-change threshold screening is a powerful tool for dimensionality reduction and feature selection in transcriptome data, as it effectively reduces the number of detected genes suitable for environmental monitoring. In addition, it is able to unmask patterns in altered genetic expression hidden by data noise and reduces the chance of type II errors, e.g., in environmental screening.
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Affiliation(s)
- Jonas Hausen
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Jens C Otte
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Monika Hammers-Wirtz
- Research Institute for Ecosystem Analysis and Assessment - gaiac, Kackertstraße 10, 52072, Aachen, Germany
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Steffen H Keiter
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Man-Technology-Environment Research Centre, Örebro University, 701 82, Örebro, Sweden
| | - Richard Ottermanns
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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Hausen J. Chemie und Chemie-Bedarf auf der Technischen Messe Hannover 1953. CHEM-ING-TECH 1953. [DOI: 10.1002/cite.330250712] [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: 11/07/2022]
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Hausen J. Rationelles Erfinden: Technische Dokumentation als Grundlage von Entwicklungsarbeiten. CHEM-ING-TECH 1952. [DOI: 10.1002/cite.330240903] [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: 11/07/2022]
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Hausen J, Bandel G, Esch W, Nitsche R, Doehring H, Staudinger H, Heuer W, Schulz GV, Kolleck L, R�hrs W, Forrer M, Amigo A, Krahl M, Rossi LM, Peakes GL, Mooney M, Speitmann M, Noll A, Kuntze W, Vieweg R, Batsch H, Meissner A, Erk S, Keller A, Poltz H, Steger W. Kunststoffe. Anal Bioanal Chem 1941. [DOI: 10.1007/bf01324136] [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: 11/29/2022]
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Hausen J. Stand und Aufgaben der Kunststoffprüfung. Angew Chem Int Ed Engl 1939. [DOI: 10.1002/ange.19390520105] [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: 11/07/2022]
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Hausen J. Die Korrosionsforschungen der Chemisch-Technischen Reichsanstalt. Angew Chem Int Ed Engl 1927. [DOI: 10.1002/ange.19270400703] [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: 11/09/2022]
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