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Abstract
Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies among muscles. Muscle-specific molecular mechanisms in healthy and normal conditions could designate changes in physiologic and pathologic conditions. We generated deep mRNA-sequencing data in adult fast and slow mouse muscles, and applying paired analysis, we identified that the muscle-specific signatures are composed of half of the muscle transcriptome. The fast muscles showed a more compact gene network that is concordant with homogenous myofiber typing, compared with the pattern in the slow muscle. The muscle-specific mRNA landscape did not correlate with alternative spicing, alternative polyadenylation, or the expression of muscle transcription factor gene networks. However, we found significant correlation between the differentially expressed noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) and their target genes. More than 25% of the genes expressed in a muscle-specific fashion were found to be targets of muscle-specific miRNAs and lncRNAs. We suggest that muscle-specific miRNAs and lncRNAs contribute to the establishment of muscle-specific transcriptomes in adult muscles.-Raz, V., Riaz, M., Tatum, Z., Kielbasa, S. M., 't Hoen, P. A. C. The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.
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Affiliation(s)
- Vered Raz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Muhammad Riaz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M Kielbasa
- Department of Medical Statistics and Bioinformatics, Bioinformatics Center of Expertise, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Suurmond J, Habets KLL, Tatum Z, Schonkeren JJ, Hoen PAC', Huizinga TWJ, Laros JFJ, Toes REM, Kurreeman F. Repeated FcεRI triggering reveals modified mast cell function related to chronic allergic responses in tissue. J Allergy Clin Immunol 2016; 138:869-880. [PMID: 27033170 DOI: 10.1016/j.jaci.2016.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 12/18/2015] [Accepted: 01/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Activation of mast cells through FcεRI plays an important role in acute allergic reactions. However, little is known about the function of mast cells in patients with chronic allergic inflammation or the effect of repeated FcεRI triggering occurring in such responses. OBJECTIVE We aimed to identify changes in mast cell function after repeated FcεRI triggering and to correlate these changes to chronic allergic responses in tissue. METHODS Human cord blood-derived mast cells were treated for 2 weeks with anti-IgE. The function of naive or treated mast cells was analyzed by means of RNA sequencing, quantitative RT-PCR, flow cytometry, and functional assays. Protein secretion was measured with ELISAs and multiplex assays. RESULTS We observed several changes in mast cell function after repeated anti-IgE triggering. Although the acute response was dampened, we identified 289 genes significantly upregulated after repeated anti-IgE. Most of these genes (84%) were not upregulated after a single anti-IgE stimulus, indicating a significantly different response mode characterized by increased antigen presentation, response to bacteria, and chemotaxis. Changes in mast cell function were related to changes in expression of the transcription factors RXRA and BATF and others. Importantly, we found a substantial overlap between genes upregulated after repeated anti-IgE triggering and genes upregulated in tissue from patients with chronic allergy, in particular those of patients with chronic rhinosinusitis. CONCLUSION Our study provides evidence for intrinsic modulation of mast cell function on repeated FcεRI-mediated activation. The overlap with gene expression in tissues is suggestive of a direct link between repeated IgE-mediated activation of mast cells and chronic allergy.
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Affiliation(s)
- Jolien Suurmond
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim L L Habets
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joris J Schonkeren
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
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Hettne KM, Thompson M, van Haagen HHHBM, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JFJ, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen GJB, Roos M, ‘t Hoen PA, Mons B, Schultes EA. The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PLoS One 2016; 11:e0149621. [PMID: 26919047 PMCID: PMC4769089 DOI: 10.1371/journal.pone.0149621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 09/22/2015] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations.
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Affiliation(s)
- Kristina M. Hettne
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Mark Thompson
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Eelke van der Horst
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eleni Mina
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F. J. Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik M. van Mulligen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martijn Schuemie
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tong Shu Li
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | | | - Benjamin M. Good
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Andrew I. Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Jan A. Kors
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gert-Jan B. van Ommen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A.C. ‘t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
| | - Erik A. Schultes
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Institute for Advanced Computer Science, Leiden, The Netherlands
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Mina E, Thompson M, Kaliyaperumal R, Zhao J, der Horst VE, Tatum Z, Hettne KM, Schultes EA, Mons B, Roos M. Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study. J Biomed Semantics 2015; 6:5. [PMID: 26464783 PMCID: PMC4603842 DOI: 10.1186/2041-1480-6-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 05/31/2014] [Accepted: 10/31/2014] [Indexed: 12/20/2022] Open
Abstract
Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, the majority of new associations are often archived either as supplemental information in an arbitrary format or in publisher-independent databases that can be difficult to find. These data are not only lost from scientific discourse, but are also elusive to automated search, retrieval and processing. Here, we use the nanopublication model to make scientific assertions that were concluded from a workflow analysis of Huntington’s Disease data machine-readable, interoperable, and citable. We followed the nanopublication guidelines to semantically model our assertions as well as their provenance metadata and authorship. We demonstrate interoperability by linking nanopublication provenance to the Research Object model. These results indicate that nanopublications can provide an incentive for researchers to expose data that is interoperable and machine-readable for future use and preservation for which they can get credits for their effort. Nanopublications can have a leading role into hypotheses generation offering opportunities to produce large-scale data integration.
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Affiliation(s)
- Eleni Mina
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Mark Thompson
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Jun Zhao
- Department of Zoology, University of Oxford, Oxford, UK
| | - van Eelke der Horst
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Kristina M Hettne
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Erik A Schultes
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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5
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Abstract
BACKGROUND Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. RESULTS As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. CONCLUSIONS We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO.
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Affiliation(s)
- Zuotian Tatum
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Marco Roos
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
- Informatics Institute of the Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Andrew P Gibson
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Peter EM Taschner
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Mark Thompson
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Erik A Schultes
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Jeroen FJ Laros
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
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Patrinos GP, Cooper DN, van Mulligen E, Gkantouna V, Tzimas G, Tatum Z, Schultes E, Roos M, Mons B. Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain. Hum Mutat 2012; 33:1503-12. [PMID: 22736453 DOI: 10.1002/humu.22144] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/23/2012] [Indexed: 11/07/2022]
Abstract
The advances in bioinformatics required to annotate human genomic variants and to place them in public data repositories have not kept pace with their discovery. Moreover, a law of diminishing returns has begun to operate both in terms of data publication and submission. Although the continued deposition of such data in the public domain is essential to maximize both their scientific and clinical utility, rewards for data sharing are few, representing a serious practical impediment to data submission. To date, two main strategies have been adopted as a means to encourage the submission of human genomic variant data: (1) database journal linkups involving the affiliation of a scientific journal with a publicly available database and (2) microattribution, involving the unambiguous linkage of data to their contributors via a unique identifier. The latter could in principle lead to the establishment of a microcitation-tracking system that acknowledges individual endeavor and achievement. Both approaches could incentivize potential data contributors, thereby encouraging them to share their data with the scientific community. Here, we summarize and critically evaluate approaches that have been proposed to address current deficiencies in data attribution and discuss ways in which they could become more widely adopted as novel scientific publication modalities.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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