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Henao JD, Lauber M, Azevedo M, Grekova A, Theis F, List M, Ogris C, Schubert B. Multi-omics regulatory network inference in the presence of missing data. Brief Bioinform 2023; 24:bbad309. [PMID: 37670505 PMCID: PMC10516394 DOI: 10.1093/bib/bbad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/06/2023] [Accepted: 05/29/2023] [Indexed: 09/07/2023] Open
Abstract
A key problem in systems biology is the discovery of regulatory mechanisms that drive phenotypic behaviour of complex biological systems in the form of multi-level networks. Modern multi-omics profiling techniques probe these fundamental regulatory networks but are often hampered by experimental restrictions leading to missing data or partially measured omics types for subsets of individuals due to cost restrictions. In such scenarios, in which missing data is present, classical computational approaches to infer regulatory networks are limited. In recent years, approaches have been proposed to infer sparse regression models in the presence of missing information. Nevertheless, these methods have not been adopted for regulatory network inference yet. In this study, we integrated regression-based methods that can handle missingness into KiMONo, a Knowledge guided Multi-Omics Network inference approach, and benchmarked their performance on commonly encountered missing data scenarios in single- and multi-omics studies. Overall, two-step approaches that explicitly handle missingness performed best for a wide range of random- and block-missingness scenarios on imbalanced omics-layers dimensions, while methods implicitly handling missingness performed best on balanced omics-layers dimensions. Our results show that robust multi-omics network inference in the presence of missing data with KiMONo is feasible and thus allows users to leverage available multi-omics data to its full extent.
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Affiliation(s)
- Juan D Henao
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Michael Lauber
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising
| | - Manuel Azevedo
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Anastasiia Grekova
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Fabian Theis
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
- Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising
| | - Christoph Ogris
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Benjamin Schubert
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
- Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
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2
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Hammad S, Ogris C, Othman A, Erdoesi P, Schmidt-Heck W, Biermayer I, Helm B, Gao Y, Piorońska W, Holland CH, D'Alessandro LA, de la Torre C, Sticht C, Al Aoua S, Theis FJ, Bantel H, Ebert MP, Klingmüller U, Hengstler JG, Dooley S, Mueller NS. Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation. Cell Death Dis 2023; 14:414. [PMID: 37438332 DOI: 10.1038/s41419-023-05855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/13/2023] [Accepted: 05/05/2023] [Indexed: 07/14/2023]
Abstract
The human liver has a remarkable capacity to regenerate and thus compensate over decades for fibrosis caused by toxic chemicals, drugs, alcohol, or malnutrition. To date, no protective mechanisms have been identified that help the liver tolerate these repeated injuries. In this study, we revealed dysregulation of lipid metabolism and mild inflammation as protective mechanisms by studying longitudinal multi-omic measurements of liver fibrosis induced by repeated CCl4 injections in mice (n = 45). Based on comprehensive proteomics, transcriptomics, blood- and tissue-level profiling, we uncovered three phases of early disease development-initiation, progression, and tolerance. Using novel multi-omic network analysis, we identified multi-level mechanisms that are significantly dysregulated in the injury-tolerant response. Public data analysis shows that these profiles are altered in human liver diseases, including fibrosis and early cirrhosis stages. Our findings mark the beginning of the tolerance phase as the critical switching point in liver response to repetitive toxic doses. After fostering extracellular matrix accumulation as an acute response, we observe a deposition of tiny lipid droplets in hepatocytes only in the Tolerant phase. Our comprehensive study shows that lipid metabolism and mild inflammation may serve as biomarkers and are putative functional requirements to resist further disease progression.
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Affiliation(s)
- Seddik Hammad
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt.
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Amnah Othman
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Pia Erdoesi
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Ina Biermayer
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Barbara Helm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Yan Gao
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Weronika Piorońska
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christian H Holland
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Lorenza A D'Alessandro
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Carolina de la Torre
- Core Facility Next Generation Sequencing, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- Core Facility Next Generation Sequencing, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Sherin Al Aoua
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heike Bantel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Jan G Hengstler
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Steven Dooley
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nikola S Mueller
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
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3
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Pardo M, Offer S, Hartner E, Di Bucchianico S, Bisig C, Bauer S, Pantzke J, Zimmermann EJ, Cao X, Binder S, Kuhn E, Huber A, Jeong S, Käfer U, Schneider E, Mesceriakovas A, Bendl J, Brejcha R, Buchholz A, Gat D, Hohaus T, Rastak N, Karg E, Jakobi G, Kalberer M, Kanashova T, Hu Y, Ogris C, Marsico A, Theis F, Shalit T, Gröger T, Rüger CP, Oeder S, Orasche J, Paul A, Ziehm T, Zhang ZH, Adam T, Sippula O, Sklorz M, Schnelle-Kreis J, Czech H, Kiendler-Scharr A, Zimmermann R, Rudich Y. Exposure to naphthalene and β-pinene-derived secondary organic aerosol induced divergent changes in transcript levels of BEAS-2B cells. Environ Int 2022; 166:107366. [PMID: 35763991 DOI: 10.1016/j.envint.2022.107366] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/13/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The health effects of exposure to secondary organic aerosols (SOAs) are still limited. Here, we investigated and compared the toxicities of soot particles (SP) coated with β-pinene SOA (SOAβPin-SP) and SP coated with naphthalene SOA (SOANap-SP) in a human bronchial epithelial cell line (BEAS-2B) residing at the air-liquid interface. SOAβPin-SP mostly contained oxygenated aliphatic compounds from β-pinene photooxidation, whereas SOANap-SP contained a significant fraction of oxygenated aromatic products under similar conditions. Following exposure, genome-wide transcriptome responses showed an Nrf2 oxidative stress response, particularly for SOANap-SP. Other signaling pathways, such as redox signaling, inflammatory signaling, and the involvement of matrix metalloproteinase, were identified to have a stronger impact following exposure to SOANap-SP. SOANap-SP also induced a stronger genotoxicity response than that of SOAβPin-SP. This study elucidated the mechanisms that govern SOA toxicity and showed that, compared to SOAs derived from a typical biogenic precursor, SOAs from a typical anthropogenic precursor have higher toxicological potency, which was accompanied with the activation of varied cellular mechanisms, such as aryl hydrocarbon receptor. This can be attributed to the difference in chemical composition; specifically, the aromatic compounds in the naphthalene-derived SOA had higher cytotoxic potential than that of the β-pinene-derived SOA.
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Affiliation(s)
- Michal Pardo
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel.
| | - Svenja Offer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Elena Hartner
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christoph Bisig
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jana Pantzke
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Elias J Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Stephanie Binder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Evelyn Kuhn
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Seongho Jeong
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Uwe Käfer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Eric Schneider
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Arunas Mesceriakovas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Jan Bendl
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Werner- Heisenberg-Weg 39, D-85577 Neubiberg, Germany; Institute for Environmental Studies, Faculty of Science, Charles University, Albertov 6, CZE-12800 Prague, Czech Republic
| | - Ramona Brejcha
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Angela Buchholz
- Department of Applied Physics, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Daniela Gat
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel
| | - Thorsten Hohaus
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Narges Rastak
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Erwin Karg
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Gert Jakobi
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Markus Kalberer
- Department of Environmental Sciences, University of Basel, Klingelbergstr. 27, CH-4056 Basel, Switzerland
| | - Tamara Kanashova
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Robert-Rössle-Str. 10, D-13125 Berlin, Germany
| | - Yue Hu
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Annalisa Marsico
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Tali Shalit
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thomas Gröger
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jürgen Orasche
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Andreas Paul
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Till Ziehm
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Zhi-Hui Zhang
- Department of Environmental Sciences, University of Basel, Klingelbergstr. 27, CH-4056 Basel, Switzerland
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Werner- Heisenberg-Weg 39, D-85577 Neubiberg, Germany
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Martin Sklorz
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jürgen Schnelle-Kreis
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hendryk Czech
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Astrid Kiendler-Scharr
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel
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Hu Y, Rehawi G, Moyon L, Gerstner N, Ogris C, Knauer-Arloth J, Bittner F, Marsico A, Mueller NS. Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection. Front Genet 2022; 13:909714. [PMID: 35903362 PMCID: PMC9315940 DOI: 10.3389/fgene.2022.909714] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
COVID-19 is a heterogeneous disease caused by SARS-CoV-2. Aside from infections of the lungs, the disease can spread throughout the body and damage many other tissues, leading to multiorgan failure in severe cases. The highly variable symptom severity is influenced by genetic predispositions and preexisting diseases which have not been investigated in a large-scale multimodal manner. We present a holistic analysis framework, setting previously reported COVID-19 genes in context with prepandemic data, such as gene expression patterns across multiple tissues, polygenetic predispositions, and patient diseases, which are putative comorbidities of COVID-19. First, we generate a multimodal network using the prior-based network inference method KiMONo. We then embed the network to generate a meaningful lower-dimensional representation of the data. The input data are obtained via the Genotype-Tissue Expression project (GTEx), containing expression data from a range of tissues with genomic and phenotypic information of over 900 patients and 50 tissues. The generated network consists of nodes, that is, genes and polygenic risk scores (PRS) for several diseases/phenotypes, as well as for COVID-19 severity and hospitalization, and links between them if they are statistically associated in a regularized linear model by feature selection. Applying network embedding on the generated multimodal network allows us to perform efficient network analysis by identifying nodes close by in a lower-dimensional space that correspond to entities which are statistically linked. By determining the similarity between COVID-19 genes and other nodes through embedding, we identify disease associations to tissues, like the brain and gut. We also find strong associations between COVID-19 genes and various diseases such as ischemic heart disease, cerebrovascular disease, and hypertension. Moreover, we find evidence linking PTPN6 to a range of comorbidities along with the genetic predisposition of COVID-19, suggesting that this kinase is a central player in severe cases of COVID-19. In conclusion, our holistic network inference coupled with network embedding of multimodal data enables the contextualization of COVID-19-associated genes with respect to tissues, disease states, and genetic risk factors. Such contextualization can be exploited to further elucidate the biological importance of known and novel genes for severity of the disease in patients.
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Affiliation(s)
- Yue Hu
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Informatics 12 Chair of Bioinformatics, Technical University Munich, Garching, Germany
| | - Ghalia Rehawi
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | - Lambert Moyon
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
| | - Nathalie Gerstner
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | - Christoph Ogris
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
| | - Janine Knauer-Arloth
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | | | - Annalisa Marsico
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- *Correspondence: Annalisa Marsico, ; Nikola S. Mueller,
| | - Nikola S. Mueller
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- knowing01 GmbH, Munich, Germany
- *Correspondence: Annalisa Marsico, ; Nikola S. Mueller,
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5
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Ogris C, Castresana-Aguirre M, Sonnhammer ELL. PathwAX II: Network-based pathway analysis with interactive visualization of network crosstalk. Bioinformatics 2022; 38:2659-2660. [PMID: 35266519 PMCID: PMC9048662 DOI: 10.1093/bioinformatics/btac153] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/03/2022] [Accepted: 03/09/2022] [Indexed: 11/28/2022] Open
Abstract
Motivation Pathway annotation tools are indispensable for the interpretation of a wide range of experiments in life sciences. Network-based algorithms have recently been developed which are more sensitive than traditional overlap-based algorithms, but there is still a lack of good online tools for network-based pathway analysis. Results We present PathwAX II—a pathway analysis web tool based on network crosstalk analysis using the BinoX algorithm. It offers several new features compared with the first version, including interactive graphical network visualization of the crosstalk between a query gene set and an enriched pathway, and the addition of Reactome pathways. Availability and implementation PathwAX II is available at http://pathwax.sbc.su.se. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christoph Ogris
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031.,Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany Ingolstädter Landstr. 1 85764
| | - Miguel Castresana-Aguirre
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031
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Offer S, Hartner E, Di Bucchianico S, Bisig C, Bauer S, Pantzke J, Zimmermann EJ, Cao X, Binder S, Kuhn E, Huber A, Jeong S, Käfer U, Martens P, Mesceriakovas A, Bendl J, Brejcha R, Buchholz A, Gat D, Hohaus T, Rastak N, Jakobi G, Kalberer M, Kanashova T, Hu Y, Ogris C, Marsico A, Theis F, Pardo M, Gröger T, Oeder S, Orasche J, Paul A, Ziehm T, Zhang ZH, Adam T, Sippula O, Sklorz M, Schnelle-Kreis J, Czech H, Kiendler-Scharr A, Rudich Y, Zimmermann R. Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air–Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs). Environ Health Perspect 2022; 130:27003. [PMID: 35112925 PMCID: PMC8812555 DOI: 10.1289/ehp9413] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background: Secondary organic aerosols (SOAs) formed from anthropogenic or biogenic gaseous precursors in the atmosphere substantially contribute to the ambient fine particulate matter [PM ≤2.5μm in aerodynamic diameter (PM2.5)] burden, which has been associated with adverse human health effects. However, there is only limited evidence on their differential toxicological impact. Objectives: We aimed to discriminate toxicological effects of aerosols generated by atmospheric aging on combustion soot particles (SPs) of gaseous biogenic (β-pinene) or anthropogenic (naphthalene) precursors in two different lung cell models exposed at the air–liquid interface (ALI). Methods: Mono- or cocultures of lung epithelial cells (A549) and endothelial cells (EA.hy926) were exposed at the ALI for 4 h to different aerosol concentrations of a photochemically aged mixture of primary combustion SP and β-pinene (SOAβPIN-SP) or naphthalene (SOANAP-SP). The internally mixed soot/SOA particles were comprehensively characterized in terms of their physical and chemical properties. We conducted toxicity tests to determine cytotoxicity, intracellular oxidative stress, primary and secondary genotoxicity, as well as inflammatory and angiogenic effects. Results: We observed considerable toxicity-related outcomes in cells treated with either SOA type. Greater adverse effects were measured for SOANAP-SP compared with SOAβPIN-SP in both cell models, whereas the nano-sized soot cores alone showed only minor effects. At the functional level, we found that SOANAP-SP augmented the secretion of malondialdehyde and interleukin-8 and may have induced the activation of endothelial cells in the coculture system. This activation was confirmed by comet assay, suggesting secondary genotoxicity and greater angiogenic potential. Chemical characterization of PM revealed distinct qualitative differences in the composition of the two secondary aerosol types. Discussion: In this study using A549 and EA.hy926 cells exposed at ALI, SOA compounds had greater toxicity than primary SPs. Photochemical aging of naphthalene was associated with the formation of more oxidized, more aromatic SOAs with a higher oxidative potential and toxicity compared with β-pinene. Thus, we conclude that the influence of atmospheric chemistry on the chemical PM composition plays a crucial role for the adverse health outcome of emissions. https://doi.org/10.1289/EHP9413
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Affiliation(s)
- Svenja Offer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Elena Hartner
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christoph Bisig
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jana Pantzke
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Elias J. Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Stefanie Binder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Evelyn Kuhn
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Seongho Jeong
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Uwe Käfer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Patrick Martens
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Arunas Mesceriakovas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jan Bendl
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Chemistry and Environmental Engineering, University of the Bundeswehr Munich, Neubiberg, Germany
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ramona Brejcha
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Angela Buchholz
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - Daniella Gat
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Thorsten Hohaus
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Narges Rastak
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gert Jakobi
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Markus Kalberer
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | | | - Yue Hu
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annalisa Marsico
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michal Pardo
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Gröger
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jürgen Orasche
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andreas Paul
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Till Ziehm
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Zhi-Hui Zhang
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Chemistry and Environmental Engineering, University of the Bundeswehr Munich, Neubiberg, Germany
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Martin Sklorz
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jürgen Schnelle-Kreis
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hendryk Czech
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Astrid Kiendler-Scharr
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
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Welz L, Kakavand N, Hang X, Laue G, Ito G, Silva MG, Plattner C, Mishra N, Tengen F, Ogris C, Jesinghaus M, Wottawa F, Arnold P, Kaikkonen L, Stengel S, Tran F, Das S, Kaser A, Trajanoski Z, Blumberg R, Roecken C, Saur D, Tschurtschenthaler M, Schreiber S, Rosenstiel P, Aden K. Epithelial X-Box Binding Protein 1 Coordinates Tumor Protein p53-Driven DNA Damage Responses and Suppression of Intestinal Carcinogenesis. Gastroenterology 2022; 162:223-237.e11. [PMID: 34599932 PMCID: PMC8678303 DOI: 10.1053/j.gastro.2021.09.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Throughout life, the intestinal epithelium undergoes constant self-renewal from intestinal stem cells. Together with genotoxic stressors and failing DNA repair, this self-renewal causes susceptibility toward malignant transformation. X-box binding protein 1 (XBP1) is a stress sensor involved in the unfolded protein response (UPR). We hypothesized that XBP1 acts as a signaling hub to regulate epithelial DNA damage responses. METHODS Data from The Cancer Genome Atlas were analyzed for association of XBP1 with colorectal cancer (CRC) survival and molecular interactions between XBP1 and p53 pathway activity. The role of XBP1 in orchestrating p53-driven DNA damage response was tested in vitro in mouse models of chronic intestinal epithelial cell (IEC) DNA damage (Xbp1/H2bfl/fl, Xbp1ΔIEC, H2bΔIEC, H2b/Xbp1ΔIEC) and via orthotopic tumor organoid transplantation. Transcriptome analysis of intestinal organoids was performed to identify molecular targets of Xbp1-mediated DNA damage response. RESULTS In The Cancer Genome Atlas data set of CRC, low XBP1 expression was significantly associated with poor overall survival and reduced p53 pathway activity. In vivo, H2b/Xbp1ΔIEC mice developed spontaneous intestinal carcinomas. Orthotopic tumor organoid transplantation revealed a metastatic potential of H2b/Xbp1ΔIEC-derived tumors. RNA sequencing of intestinal organoids (H2b/Xbp1fl/fl, H2bΔIEC, H2b/Xbp1ΔIEC, and H2b/p53ΔIEC) identified a transcriptional program downstream of p53, in which XBP1 directs DNA-damage-inducible transcript 4-like (Ddit4l) expression. DDIT4L inhibits mechanistic target of rapamycin-mediated phosphorylation of 4E-binding protein 1. Pharmacologic mechanistic target of rapamycin inhibition suppressed epithelial hyperproliferation via 4E-binding protein 1. CONCLUSIONS Our data suggest a crucial role for XBP1 in coordinating epithelial DNA damage responses and stem cell function via a p53-DDIT4L-dependent feedback mechanism.
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Affiliation(s)
- Lina Welz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nassim Kakavand
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Xiang Hang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Georg Laue
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miguel Gomes Silva
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Christina Plattner
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Felicitas Tengen
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, University Hospital Marburg, Marburg, Germany
| | - Felix Wottawa
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Leena Kaikkonen
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Stefanie Stengel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Blumberg
- Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christoph Roecken
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Markus Tschurtschenthaler
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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8
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Ogris C, Hu Y, Arloth J, Müller NS. Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data. Sci Rep 2021; 11:6806. [PMID: 33762588 PMCID: PMC7990936 DOI: 10.1038/s41598-021-85544-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/04/2021] [Indexed: 12/28/2022] Open
Abstract
Constantly decreasing costs of high-throughput profiling on many molecular levels generate vast amounts of multi-omics data. Studying one biomedical question on two or more omic levels provides deeper insights into underlying molecular processes or disease pathophysiology. For the majority of multi-omics data projects, the data analysis is performed level-wise, followed by a combined interpretation of results. Hence the full potential of integrated data analysis is not leveraged yet, presumably due to the complexity of the data and the lacking toolsets. We propose a versatile approach, to perform a multi-level fully integrated analysis: The Knowledge guIded Multi-Omics Network inference approach, KiMONo (https://github.com/cellmapslab/kimono). KiMONo performs network inference by using statistical models for combining omics measurements coupled to a powerful knowledge-guided strategy exploiting prior information from existing biological sources. Within the resulting multimodal network, nodes represent features of all input types e.g. variants and genes while edges refer to knowledge-supported and statistically derived associations. In a comprehensive evaluation, we show that our method is robust to noise and exemplify the general applicability to the full spectrum of multi-omics data, demonstrating that KiMONo is a powerful approach towards leveraging the full potential of data sets for detecting biomarker candidates.
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Affiliation(s)
- Christoph Ogris
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Yue Hu
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Janine Arloth
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Translational Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Nikola S Müller
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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9
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Acevedo N, Scala G, Merid SK, Frumento P, Bruhn S, Andersson A, Ogris C, Bottai M, Pershagen G, Koppelman GH, Melén E, Sonnhammer E, Alm J, Söderhäll C, Kere J, Greco D, Scheynius A. DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life. Int J Mol Sci 2021; 22:ijms22020801. [PMID: 33466918 PMCID: PMC7830007 DOI: 10.3390/ijms22020801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/23/2022] Open
Abstract
DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.
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Affiliation(s)
- Nathalie Acevedo
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute for Immunological Research, University of Cartagena, 130014 Cartagena, Colombia
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, 80138 Napoli, Italy;
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
| | - Simon Kebede Merid
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Paolo Frumento
- Department of Political Sciences, University of Pisa, 56126 Pisa, Italy;
| | - Sören Bruhn
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Anna Andersson
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Matteo Bottai
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Gerard H. Koppelman
- Section of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Erik Melén
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Erik Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
| | - Johan Alm
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Folkhälsan Research Institute, Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Correspondence:
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10
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Ogris C, Guala D, Sonnhammer ELL. FunCoup 4: new species, data, and visualization. Nucleic Acids Res 2019; 46:D601-D607. [PMID: 29165593 PMCID: PMC5755233 DOI: 10.1093/nar/gkx1138] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis. The latter allows us to also introduce a new class of functional association between genes - co-occurrence in the same operon. We also supplemented the existing classes of functional association: metabolic, signaling, complex and physical protein interaction with up-to-date information. In this release we switched to InParanoid v8 as the source of orthology and base for calculation of phylogenetic profiles. While populating all other evidence types with new data we introduce a new evidence type based on quantitative mass spectrometry data. Finally, the new JavaScript based network viewer provides the user an intuitive and responsive platform to further evaluate the results.
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Affiliation(s)
- Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Dimitri Guala
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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Guala D, Ogris C, Müller N, Sonnhammer ELL. Genome-wide functional association networks: background, data & state-of-the-art resources. Brief Bioinform 2019; 21:1224-1237. [PMID: 31281921 PMCID: PMC7373183 DOI: 10.1093/bib/bbz064] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 02/05/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/06/2023] Open
Abstract
The vast amount of experimental data from recent advances in the field of high-throughput biology begs for integration into more complex data structures such as genome-wide functional association networks. Such networks have been used for elucidation of the interplay of intra-cellular molecules to make advances ranging from the basic science understanding of evolutionary processes to the more translational field of precision medicine. The allure of the field has resulted in rapid growth of the number of available network resources, each with unique attributes exploitable to answer different biological questions. Unfortunately, the high volume of network resources makes it impossible for the intended user to select an appropriate tool for their particular research question. The aim of this paper is to provide an overview of the underlying data and representative network resources as well as to mention methods of integration, allowing a customized approach to resource selection. Additionally, this report will provide a primer for researchers venturing into the field of network integration.
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Affiliation(s)
- Dimitri Guala
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Christoph Ogris
- Computational Cell Maps, Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Nikola Müller
- Computational Cell Maps, Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Erik L L Sonnhammer
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden
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Asim M, Tarish F, Zecchini HI, Sanjiv K, Gelali E, Massie CE, Baridi A, Warren AY, Zhao W, Ogris C, McDuffus LA, Mascalchi P, Shaw G, Dev H, Wadhwa K, Wijnhoven P, Forment JV, Lyons SR, Lynch AG, O'Neill C, Zecchini VR, Rennie PS, Baniahmad A, Tavaré S, Mills IG, Galanty Y, Crosetto N, Schultz N, Neal D, Helleday T. Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer. Nat Commun 2017; 8:374. [PMID: 28851861 PMCID: PMC5575038 DOI: 10.1038/s41467-017-00393-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
Emerging data demonstrate homologous recombination (HR) defects in castration-resistant prostate cancers, rendering these tumours sensitive to PARP inhibition. Here we demonstrate a direct requirement for the androgen receptor (AR) to maintain HR gene expression and HR activity in prostate cancer. We show that PARP-mediated repair pathways are upregulated in prostate cancer following androgen-deprivation therapy (ADT). Furthermore, upregulation of PARP activity is essential for the survival of prostate cancer cells and we demonstrate a synthetic lethality between ADT and PARP inhibition in vivo. Our data suggest that ADT can functionally impair HR prior to the development of castration resistance and that, this potentially could be exploited therapeutically using PARP inhibitors in combination with androgen-deprivation therapy upfront in advanced or high-risk prostate cancer.Tumours with homologous recombination (HR) defects become sensitive to PARPi. Here, the authors show that androgen receptor (AR) regulates HR and AR inhibition activates the PARP pathway in vivo, thus inhibition of both AR and PARP is required for effective treatment of high risk prostate cancer.
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Affiliation(s)
- Mohammad Asim
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, GU2 7WG, UK.
| | - Firas Tarish
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
- Department of Urology, Central Hospital, 721 89, Västerås, Sweden
| | - Heather I Zecchini
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Kumar Sanjiv
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Eleni Gelali
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Charles E Massie
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Ajoeb Baridi
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, CB2 0QQ, UK
| | - Wanfeng Zhao
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, CB2 0QQ, UK
| | - Christoph Ogris
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Leigh-Anne McDuffus
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Patrice Mascalchi
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Greg Shaw
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Harveer Dev
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Karan Wadhwa
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Paul Wijnhoven
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Josep V Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Scott R Lyons
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Andy G Lynch
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Cormac O'Neill
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Vincent R Zecchini
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Paul S Rennie
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada, V6H 3Z6
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, 07743, Jena, Germany
| | - Simon Tavaré
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, 0318, Oslo, Norway
- Prostate Cancer UK/Movember Centre of Excellence, Queen's University, Belfast, BT9 7AE, UK
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nicola Crosetto
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Niklas Schultz
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - David Neal
- Cancer Research UK Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- Nuffield Department of Surgery, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden.
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Ogris C, Guala D, Helleday T, Sonnhammer ELL. A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation. Nucleic Acids Res 2016; 45:e8. [PMID: 27664219 PMCID: PMC5314790 DOI: 10.1093/nar/gkw849] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 12/13/2022] Open
Abstract
Analyzing gene expression patterns is a mainstay to gain functional insights of biological systems. A plethora of tools exist to identify significant enrichment of pathways for a set of differentially expressed genes. Most tools analyze gene overlap between gene sets and are therefore severely hampered by the current state of pathway annotation, yet at the same time they run a high risk of false assignments. A way to improve both true positive and false positive rates (FPRs) is to use a functional association network and instead look for enrichment of network connections between gene sets. We present a new network crosstalk analysis method BinoX that determines the statistical significance of network link enrichment or depletion between gene sets, using the binomial distribution. This is a much more appropriate statistical model than previous methods have employed, and as a result BinoX yields substantially better true positive and FPRs than was possible before. A number of benchmarks were performed to assess the accuracy of BinoX and competing methods. We demonstrate examples of how BinoX finds many biologically meaningful pathway annotations for gene sets from cancer and other diseases, which are not found by other methods. BinoX is available at http://sonnhammer.org/BinoX.
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Affiliation(s)
- Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Dimitri Guala
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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Ogris C, Helleday T, Sonnhammer ELL. PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res 2016; 44:W105-9. [PMID: 27151197 PMCID: PMC4987909 DOI: 10.1093/nar/gkw356] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/19/2016] [Indexed: 12/22/2022] Open
Abstract
Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the challenge is to compare a given gene list with the known pathways such that all true relations are identified. Most tools apply statistical measures to the gene overlap between the gene list and pathway. It is however problematic to avoid false negatives and false positives when only using the gene overlap. The pathwAX web server (http://pathwAX.sbc.su.se/) applies a different approach which is based on network crosstalk. It uses the comprehensive network FunCoup to analyse network crosstalk between a query gene list and KEGG pathways. PathwAX runs the BinoX algorithm, which employs Monte-Carlo sampling of randomized networks and estimates a binomial distribution, for estimating the statistical significance of the crosstalk. This results in substantially higher accuracy than gene overlap methods. The system was optimized for speed and allows interactive web usage. We illustrate the usage and output of pathwAX.
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Affiliation(s)
- Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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Abstract
We present an update of the FunCoup database (http://FunCoup.sbc.su.se) of functional couplings, or functional associations, between genes and gene products. Identifying these functional couplings is an important step in the understanding of higher level mechanisms performed by complex cellular processes. FunCoup distinguishes between four classes of couplings: participation in the same signaling cascade, participation in the same metabolic process, co-membership in a protein complex and physical interaction. For each of these four classes, several types of experimental and statistical evidence are combined by Bayesian integration to predict genome-wide functional coupling networks. The FunCoup framework has been completely re-implemented to allow for more frequent future updates. It contains many improvements, such as a regularization procedure to automatically downweight redundant evidences and a novel method to incorporate phylogenetic profile similarity. Several datasets have been updated and new data have been added in FunCoup 3.0. Furthermore, we have developed a new Web site, which provides powerful tools to explore the predicted networks and to retrieve detailed information about the data underlying each prediction.
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Affiliation(s)
- Thomas Schmitt
- Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, Solna SE-17121, Sweden, Department of Biochemistry and Biophysics, Stockholm University and Swedish eScience Research Center
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