1
|
Oveland E, Ahmad I, Lereim RR, Kroksveen AC, Barsnes H, Guldbrandsen A, Myhr KM, Bø L, Berven FS, Wergeland S. Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Sci Rep 2021; 11:7174. [PMID: 33785790 PMCID: PMC8010076 DOI: 10.1038/s41598-021-86191-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
Two pathophysiological different experimental models for multiple sclerosis were analyzed in parallel using quantitative proteomics in attempts to discover protein alterations applicable as diagnostic-, prognostic-, or treatment targets in human disease. The cuprizone model reflects de- and remyelination in multiple sclerosis, and the experimental autoimmune encephalomyelitis (EAE, MOG1-125) immune-mediated events. The frontal cortex, peripheral to severely inflicted areas in the CNS, was dissected and analyzed. The frontal cortex had previously not been characterized by proteomics at different disease stages, and novel protein alterations involved in protecting healthy tissue and assisting repair of inflicted areas might be discovered. Using TMT-labelling and mass spectrometry, 1871 of the proteins quantified overlapped between the two experimental models, and the fold change compared to controls was verified using label-free proteomics. Few similarities in frontal cortex between the two disease models were observed when regulated proteins and signaling pathways were compared. Legumain and C1Q complement proteins were among the most upregulated proteins in cuprizone and hemopexin in the EAE model. Immunohistochemistry showed that legumain expression in post-mortem multiple sclerosis brain tissue (n = 19) was significantly higher in the center and at the edge of white matter active and chronic active lesions. Legumain was associated with increased lesion activity and might be valuable as a drug target using specific inhibitors as already suggested for Parkinson's and Alzheimer's disease. Cerebrospinal fluid levels of legumain, C1q and hemopexin were not significantly different between multiple sclerosis patients, other neurological diseases, or healthy controls.
Collapse
Affiliation(s)
- Eystein Oveland
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
| | - Intakhar Ahmad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ann Cathrine Kroksveen
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Kjell-Morten Myhr
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Lars Bø
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
| | - Stig Wergeland
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway.
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
2
|
Interferon-Stimulated Genes-Mediators of the Innate Immune Response during Canine Distemper Virus Infection. Int J Mol Sci 2019; 20:ijms20071620. [PMID: 30939763 PMCID: PMC6480560 DOI: 10.3390/ijms20071620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
The demyelinating canine distemper virus (CDV)-leukoencephalitis represents a translational animal model for multiple sclerosis. The present study investigated the expression of type I interferon (IFN-I) pathway members in CDV-induced cerebellar lesions to gain an insight into their role in lesion development. Gene expression of 110 manually selected genes in acute, subacute and chronic lesions was analyzed using pre-existing microarray data. Interferon regulatory factor (IRF) 3, IRF7, signal transducer and activator of transcription (STAT) 1, STAT2, MX protein, protein kinase R (PKR), 2'-5'-oligoadenylate synthetase (OAS) 1 and interferon-stimulated gene (ISG) 15 expression were also evaluated using immunohistochemistry. Cellular origin of STAT1, STAT2, MX and PKR were determined using immunofluorescence. CDV infection caused an increased expression of the antiviral effector proteins MX, PKR, OAS1 and ISG15, which probably contributed to a restricted viral replication, particularly in neurons and oligodendrocytes. This increase might be partly mediated by IRF-dependent pathways due to the lack of changes in IFN-I levels and absence of STAT2 in astrocytes. Nevertheless, activated microglia/macrophages showed a strong expression of STAT1, STAT2 and MX proteins in later stages of the disease, indicating a strong activation of the IFN-I signaling cascade, which might be involved in the aggravation of bystander demyelination.
Collapse
|
3
|
Heinrich F, Lehmbecker A, Raddatz BB, Kegler K, Tipold A, Stein VM, Kalkuhl A, Deschl U, Baumgärtner W, Ulrich R, Spitzbarth I. Morphologic, phenotypic, and transcriptomic characterization of classically and alternatively activated canine blood-derived macrophages in vitro. PLoS One 2017; 12:e0183572. [PMID: 28817687 PMCID: PMC5560737 DOI: 10.1371/journal.pone.0183572] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
Macrophages are a heterogeneous cell population playing a pivotal role in tissue homeostasis and inflammation, and their phenotype strongly depends on the micromilieu. Despite its increasing importance as a translational animal model for human diseases, there is a considerable gap of knowledge with respect to macrophage polarization in dogs. The present study comprehensively investigated the morphologic, phenotypic, and transcriptomic characteristics of unstimulated (M0), M1- (GM-CSF, LPS, IFNγ-stimulated) and M2- (M-CSF, IL-4-stimulated)-polarized canine blood-derived macrophages in vitro. Scanning electron microscopy revealed distinct morphologies of polarized macrophages with formation of multinucleated cells in M2-macrophages, while immunofluorescence employing literature-based prototype-antibodies against CD16, CD32, iNOS, MHC class II (M1-markers), CD163, CD206, and arginase-1 (M2-markers) demonstrated that only CD206 was able to discriminate M2-macrophages from both other phenotypes, highlighting this molecule as a promising marker for canine M2-macrophages. Global microarray analysis revealed profound changes in the transcriptome of polarized canine macrophages. Functional analysis pointed out that M1-polarization was associated with biological processes such as "respiratory burst", whereas M2-polarization was associated with processes such as "mitosis". Literature-based marker gene selection revealed only minor overlaps in the gene sets of the dog compared to prototype markers of murine and human macrophages. Biomarker selection using supervised clustering suggested latexin (LXN) and membrane-spanning 4-domains, subfamily A, member 2 (MS4A2) to be the most powerful predicting biomarkers for canine M1- and M2-macrophages, respectively. Immunofluorescence for both markers demonstrated expression of both proteins by macrophages in vitro but failed to reveal differences between canine M1 and M2-macrophages. The present study provides a solid basis for future studies upon the role of macrophage polarization in spontaneous diseases of the dog, a species that has emerging importance for translational research.
Collapse
Affiliation(s)
- Franziska Heinrich
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| | - Annika Lehmbecker
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| | - Barbara B. Raddatz
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| | - Kristel Kegler
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| | - Andrea Tipold
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover Foundation, Bünteweg 2, Hannover, Germany
| | - Veronika M. Stein
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
- Department of Clinical Veterinary Sciences, Vetsuisse Faculty, University of Bern, Laenggassstrasse 128, Bern, Switzerland
| | - Arno Kalkuhl
- Boehringer Ingelheim Pharma GmbH & Co.KG, Department of Non-clinical Drug Safety, Birkendorfer Str. 65, Biberach, Germany
| | - Ulrich Deschl
- Boehringer Ingelheim Pharma GmbH & Co.KG, Department of Non-clinical Drug Safety, Birkendorfer Str. 65, Biberach, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| | - Reiner Ulrich
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Friedrich-Loeffler-Institute, Department of Experimental Animal Facilities and Biorisk Management, Südufer 10, Greifswald, Germany
| | - Ingo Spitzbarth
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17, Hannover, Germany
- Center for Systems Neuroscience, Bünteweg 2, Hannover, Germany
| |
Collapse
|
4
|
Oveland E, Nystad A, Berven F, Myhr KM, Torkildsen Ø, Wergeland S. 1,25-Dihydroxyvitamin-D3 induces brain proteomic changes in cuprizone mice during remyelination involving calcium proteins. Neurochem Int 2017; 112:267-277. [PMID: 28818673 DOI: 10.1016/j.neuint.2017.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 07/20/2017] [Accepted: 08/11/2017] [Indexed: 01/15/2023]
Abstract
Dietary supplementation of vitamin D is commonly recommended to patients with multiple sclerosis. We recently found that high-dose of the hormonally active 1,25-dihydroxyvitamin-D3 (1,25D) promotes myelin repair in the cuprizone model for de- and remyelination. In the present study, we quantified 5062 proteins, of which 125 were differentially regulated in brain tissue from 1,25D treated mice during remyelination, compared to placebo. Proteins upregulated in the early remyelination phase were involved in calcium binding, e.g. calretinin (>1.3 fold, p < 0.005), S10A5 and secretagogin, and involved in mitochondrial function, e.g. NADH-ubiquinone oxidoreductase chain 3, and acyl-coenzyme A synthetase. Calretinin, S10A5 and secretagogin expression levels were characterized using immunohistochemistry. Calretinin immunoreactivity was significantly increased (>3 fold, p = 0.016) in the medial septal nuclei of 1,25D treated mice in the early remyelination phase. Our results indicate that vitamin D may influence remyelination by mechanisms involving an increase in calretinin expression and potentially other calcium binding proteins.
Collapse
Affiliation(s)
- Eystein Oveland
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Norway; Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Agnes Nystad
- Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Frode Berven
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Norway; Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kjell-Morten Myhr
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Øivind Torkildsen
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Stig Wergeland
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
5
|
Pfankuche VM, Spitzbarth I, Lapp S, Ulrich R, Deschl U, Kalkuhl A, Baumgärtner W, Puff C. Reduced angiogenic gene expression in morbillivirus-triggered oncolysis in a translational model for histiocytic sarcoma. J Cell Mol Med 2016; 21:816-830. [PMID: 27860224 PMCID: PMC5345635 DOI: 10.1111/jcmm.13023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/30/2016] [Indexed: 12/19/2022] Open
Abstract
Histiocytic sarcoma represents a rare malignant tumour with a short survival time, indicating the need of novel treatment strategies including oncolytic virotherapy. The underlying molecular mechanisms of viral oncolysis are largely unknown. As cancer in companion animals shares striking similarities with human counterparts, we chose a permanent canine histiocytic sarcoma cell line (DH82 cells) to identify global transcriptome changes following infection with canine distemper virus (CDV), a paramyxovirus closely related to human measles virus. Microarray analysis identified 3054 differentially expressed probe sets (DEPs), encoding for 892 up‐ and 869 down‐regulated unique canine genes, respectively, in DH82 cells persistently infected with the vaccine strain Onderstepoort of CDV (DH82‐Ond‐pi), compared to non‐infected DH82 cells. Up‐regulated genes were predominantly related to immune processes, as demonstrated by functional enrichment analysis. Moreover, there was substantial enrichment of genes characteristic for classically activated M1 and alternatively activated M2 macrophages in DH82‐Ond‐pi; however, significant polarization into either of both categories was lacking. ‘Angiogenesis’ was the dominant enriched functional term for the down‐regulated genes, highlighting decreased blood vessel generation as a potential mechanism of paramyxovirus‐induced oncolysis in DH82 cells. The anti‐angiogenic effect of infection was verified by immunohistochemistry, which revealed a lower blood vessel density in an in vivo mouse model, xenotransplanted with DH82‐Ond‐pi, compared to mice transplanted with non‐infected DH82 cells. Reduction in angiogenesis appears to be an important oncolytic mechanism of CDV in DH82 cells, suggesting that similar mechanisms might account for human histiocytic sarcoma and maybe other tumours in conjunction with measles virus.
Collapse
Affiliation(s)
| | - Ingo Spitzbarth
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Stefanie Lapp
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Reiner Ulrich
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Ulrich Deschl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riß), Germany
| | - Arno Kalkuhl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riß), Germany
| | | | - Christina Puff
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| |
Collapse
|
6
|
Lazzarini N, Widera P, Williamson S, Heer R, Krasnogor N, Bacardit J. Functional networks inference from rule-based machine learning models. BioData Min 2016; 9:28. [PMID: 27597880 PMCID: PMC5011349 DOI: 10.1186/s13040-016-0106-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/11/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Functional networks play an important role in the analysis of biological processes and systems. The inference of these networks from high-throughput (-omics) data is an area of intense research. So far, the similarity-based inference paradigm (e.g. gene co-expression) has been the most popular approach. It assumes a functional relationship between genes which are expressed at similar levels across different samples. An alternative to this paradigm is the inference of relationships from the structure of machine learning models. These models are able to capture complex relationships between variables, that often are different/complementary to the similarity-based methods. RESULTS We propose a protocol to infer functional networks from machine learning models, called FuNeL. It assumes, that genes used together within a rule-based machine learning model to classify the samples, might also be functionally related at a biological level. The protocol is first tested on synthetic datasets and then evaluated on a test suite of 8 real-world datasets related to human cancer. The networks inferred from the real-world data are compared against gene co-expression networks of equal size, generated with 3 different methods. The comparison is performed from two different points of view. We analyse the enriched biological terms in the set of network nodes and the relationships between known disease-associated genes in a context of the network topology. The comparison confirms both the biological relevance and the complementary character of the knowledge captured by the FuNeL networks in relation to similarity-based methods and demonstrates its potential to identify known disease associations as core elements of the network. Finally, using a prostate cancer dataset as a case study, we confirm that the biological knowledge captured by our method is relevant to the disease and consistent with the specialised literature and with an independent dataset not used in the inference process. AVAILABILITY The implementation of our network inference protocol is available at: http://ico2s.org/software/funel.html.
Collapse
Affiliation(s)
- Nicola Lazzarini
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Paweł, Widera
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Stuart Williamson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
7
|
Seehusen F, Al-Azreg SA, Raddatz BB, Haist V, Puff C, Spitzbarth I, Ulrich R, Baumgärtner W. Accumulation of Extracellular Matrix in Advanced Lesions of Canine Distemper Demyelinating Encephalitis. PLoS One 2016; 11:e0159752. [PMID: 27441688 PMCID: PMC4956304 DOI: 10.1371/journal.pone.0159752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/07/2016] [Indexed: 11/18/2022] Open
Abstract
In demyelinating diseases, changes in the quality and quantity of the extracellular matrix (ECM) may contribute to demyelination and failure of myelin repair and axonal sprouting, especially in chronic lesions. To characterize changes in the ECM in canine distemper demyelinating leukoencephalitis (DL), histochemical and immunohistochemical investigations of formalin-fixed paraffin-embedded cerebella using azan, picrosirius red and Gomori`s silver stain as well as antibodies directed against aggrecan, type I and IV collagen, fibronectin, laminin and phosphacan showed alterations of the ECM in CDV-infected dogs. A significantly increased amount of aggrecan was detected in early and late white matter lesions. In addition, the positive signal for collagens I and IV as well as fibronectin was significantly increased in late lesions. Conversely, the expression of phosphacan was significantly decreased in early and more pronounced in late lesions compared to controls. Furthermore, a set of genes involved in ECM was extracted from a publically available microarray data set and was analyzed for differential gene expression. Gene expression of ECM molecules, their biosynthesis pathways, and pro-fibrotic factors was mildly up-regulated whereas expression of matrix remodeling enzymes was up-regulated to a relatively higher extent. Summarized, the observed findings indicate that changes in the quality and content of ECM molecules represent important, mainly post-transcriptional features in advanced canine distemper lesions. Considering the insufficiency of morphological regeneration in chronic distemper lesions, the accumulated ECM seems to play a crucial role upon regenerative processes and may explain the relatively small regenerative potential in late stages of this disease.
Collapse
Affiliation(s)
- Frauke Seehusen
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Seham A. Al-Azreg
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Barbara B. Raddatz
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Verena Haist
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
- Boehringer Ingelheim Veterinary Research Center GmbH & Co. KG, Hannover, Germany
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Ingo Spitzbarth
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Reiner Ulrich
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
- * E-mail:
| |
Collapse
|
8
|
Spitzbarth I, Lempp C, Kegler K, Ulrich R, Kalkuhl A, Deschl U, Baumgärtner W, Seehusen F. Immunohistochemical and transcriptome analyses indicate complex breakdown of axonal transport mechanisms in canine distemper leukoencephalitis. Brain Behav 2016; 6:e00472. [PMID: 27247850 PMCID: PMC4864272 DOI: 10.1002/brb3.472] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/24/2016] [Accepted: 03/11/2016] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION CDV-DL (Canine distemper virus-induced demyelinating leukoencephalitis) represents a spontaneously occurring animal model for demyelinating disorders. Axonopathy represents a key pathomechanism in this disease; however, its underlying pathogenesis has not been addressed in detail so far. This study aimed at the characterization of axonal cytoskeletal, transport, and potential regenerative changes with a parallel focus upon Schwann cell remyelination. METHODS Immunohistochemistry of canine cerebellar tissue as well as a comparative analysis of genes from an independent microarray study were performed. RESULTS Increased axonal immunoreactivity for nonphosphorylated neurofilament was followed by loss of cytoskeletal and motor proteins. Interestingly, a subset of genes encoding for neurofilament subunits and motor proteins was up-regulated in the chronic stage compared to dogs with subacute CDV-DL. However, immunohistochemically, hints for axonal regeneration were restricted to up-regulated axonal positivity of hypoxia-inducible factor 1 alpha, while growth-associated protein 43, erythropoietin and its receptor were not or even down-regulated. Periaxin-positive structures, indicative of Schwann cell remyelination, were only detected within few advanced lesions. CONCLUSIONS The present findings demonstrate a complex sequence of axonal cytoskeletal breakdown mechanisms. Moreover, though sparse, this is the first report of Schwann cell remyelination in CDV-DL. Facilitation of these very limited endogenous regenerative responses represents an important topic for future research.
Collapse
Affiliation(s)
- Ingo Spitzbarth
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany; Center for Systems Neuroscience Bünteweg 2 30559 Hannover Germany
| | - Charlotte Lempp
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany
| | - Kristel Kegler
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany; Center for Systems Neuroscience Bünteweg 2 30559 Hannover Germany
| | - Reiner Ulrich
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany; Center for Systems Neuroscience Bünteweg 2 30559 Hannover Germany
| | - Arno Kalkuhl
- Department of Non-Clinical Drug Safety Boehringer Ingelheim Pharma GmbH & Co KG Biberach (Riß) Germany
| | - Ulrich Deschl
- Department of Non-Clinical Drug Safety Boehringer Ingelheim Pharma GmbH & Co KG Biberach (Riß) Germany
| | - Wolfgang Baumgärtner
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany; Center for Systems Neuroscience Bünteweg 2 30559 Hannover Germany
| | - Frauke Seehusen
- Department of Pathology University of Veterinary Medicine Hannover Foundation Bünteweg 17 30559 Hannover Germany
| |
Collapse
|
9
|
Chesneau M, Michel L, Dugast E, Chenouard A, Baron D, Pallier A, Durand J, Braza F, Guerif P, Laplaud DA, Soulillou JP, Giral M, Degauque N, Chiffoleau E, Brouard S. Tolerant Kidney Transplant Patients Produce B Cells with Regulatory Properties. J Am Soc Nephrol 2015; 26:2588-98. [PMID: 25644114 PMCID: PMC4587683 DOI: 10.1681/asn.2014040404] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 12/11/2014] [Indexed: 12/14/2022] Open
Abstract
Whereas a B cell-transcriptional profile has been recorded for operationally tolerant kidney graft patients, the role that B cells have in this tolerance has not been reported. In this study, we analyzed the role of B cells from operationally tolerant patients, healthy volunteers, and kidney transplant recipients with stable graft function on T cell suppression. Proliferation, apoptosis, and type I proinflammatory cytokine production by effector CD4(+)CD25(-) T cells were measured after anti-CD3/anti-CD28 stimulation with or without autologous B cells. We report that B cells inhibit CD4(+)CD25(-) effector T cell response in a dose-dependent manner. This effect required B cells to interact with T-cell targets and was achieved through a granzyme B (GzmB)-dependent pathway. Tolerant recipients harbored a higher number of B cells expressing GzmB and displaying a plasma cell phenotype. Finally, GzmB(+) B-cell number was dependent on IL-21 production, and B cells from tolerant recipients but not from other patients positively regulated both the number of IL-21(+) T cells and IL-21 production, suggesting a feedback loop in tolerant recipients that increases excessive B cell activation and allows regulation to take place. These data provide insights into the characterization of B cell-mediated immunoregulation in clinical tolerance and show a potential regulatory effect of B cells on effector T cells in blood from patients with operationally tolerant kidney grafts.
Collapse
Affiliation(s)
- Mélanie Chesneau
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Laure Michel
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - Emilie Dugast
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - Alexis Chenouard
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Daniel Baron
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Annaïck Pallier
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France
| | - Justine Durand
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Faouzi Braza
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Pierrick Guerif
- Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - David-Axel Laplaud
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - Jean-Paul Soulillou
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - Magali Giral
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| | - Nicolas Degauque
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Elise Chiffoleau
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and
| | - Sophie Brouard
- Joint Research Unit 1064, French Institute of Health and Medical Research, Nantes, France; Faculty of Medicine, Nantes University, Nantes, France; and Institute of Transplantation Urology and Nephrology, Nantes University Hospital, Nantes, France
| |
Collapse
|
10
|
Laing EE, Johnston JD, Möller-Levet CS, Bucca G, Smith CP, Dijk DJ, Archer SN. Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health. Bioessays 2015; 37:544-56. [PMID: 25772847 PMCID: PMC5031210 DOI: 10.1002/bies.201400193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The power of the application of bioinformatics across multiple publicly available transcriptomic data sets was explored. Using 19 human and mouse circadian transcriptomic data sets, we found that NR1D1 and NR1D2 which encode heme‐responsive nuclear receptors are the most rhythmic transcripts across sleep conditions and tissues suggesting that they are at the core of circadian rhythm generation. Analyzes of human transcriptomic data show that a core set of transcripts related to processes including immune function, glucocorticoid signalling, and lipid metabolism is rhythmically expressed independently of the sleep‐wake cycle. We also identify key transcripts associated with transcription and translation that are disrupted by sleep manipulations, and through network analysis identify putative mechanisms underlying the adverse health outcomes associated with sleep disruption, such as diabetes and cancer. Comparative bioinformatics applied to existing and future data sets will be a powerful tool for the identification of core circadian‐ and sleep‐dependent molecules.
Collapse
Affiliation(s)
- Emma E Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | | | | | | | | | | | | |
Collapse
|
11
|
Sun Y, Lehmbecker A, Kalkuhl A, Deschl U, Sun W, Rohn K, Tzvetanova ID, Nave KA, Baumgärtner W, Ulrich R. STAT3 represents a molecular switch possibly inducing astroglial instead of oligodendroglial differentiation of oligodendroglial progenitor cells in Theiler's murine encephalomyelitis. Neuropathol Appl Neurobiol 2015; 41:347-70. [DOI: 10.1111/nan.12133] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/02/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Yanyong Sun
- Department of Pathology; University of Veterinary Medicine Hannover; Hannover Germany
- Centre for Systems Neuroscience Hannover; Hannover Germany
| | - Annika Lehmbecker
- Department of Pathology; University of Veterinary Medicine Hannover; Hannover Germany
- Centre for Systems Neuroscience Hannover; Hannover Germany
| | - Arno Kalkuhl
- Department of Non-Clinical Drug Safety; Boehringer Ingelheim Pharma; Biberach (Riß) Germany
| | - Ulrich Deschl
- Department of Non-Clinical Drug Safety; Boehringer Ingelheim Pharma; Biberach (Riß) Germany
| | - Wenhui Sun
- Department of Pathology; University of Veterinary Medicine Hannover; Hannover Germany
- Centre for Systems Neuroscience Hannover; Hannover Germany
| | - Karl Rohn
- Department of Biometry, Epidemiology and Information Processing; University of Veterinary Medicine Hannover; Hannover Germany
| | - Iva D. Tzvetanova
- Department of Neurogenetics; Max Planck Institute of Experimental Medicine; Göttingen Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics; Max Planck Institute of Experimental Medicine; Göttingen Germany
| | - Wolfgang Baumgärtner
- Department of Pathology; University of Veterinary Medicine Hannover; Hannover Germany
- Centre for Systems Neuroscience Hannover; Hannover Germany
| | - Reiner Ulrich
- Department of Pathology; University of Veterinary Medicine Hannover; Hannover Germany
- Centre for Systems Neuroscience Hannover; Hannover Germany
| |
Collapse
|
12
|
Jamil HM. Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:473-486. [PMID: 26357233 DOI: 10.1109/tcbb.2014.2355213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Traditionally, biological objects such as genes, proteins, and pathways are represented by a convenient identifier, or ID, which is then used to cross reference, link and describe objects in biological databases. Relationships among the objects are often established using non-trivial and computationally complex ID mapping systems or converters, and are stored in authoritative databases such as UniGene, GeneCards, PIR and BioMart. Despite best efforts, such mappings are largely incomplete and riddled with false negatives. Consequently, data integration using record linkage that relies on these mappings produces poor quality of data, inadvertently leading to erroneous conclusions. In this paper, we discuss this largely ignored dimension of data integration, examine how the ubiquitous use of identifiers in biological databases is a significant barrier to knowledge fusion using distributed computational pipelines, and propose two algorithms for ad hoc and restriction free ID mapping of arbitrary types using online resources. We also propose two declarative statements for ID conversion and data integration based on ID mapping on-the-fly.
Collapse
|
13
|
A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft. Kidney Int 2015; 87:984-95. [PMID: 25629549 PMCID: PMC4424816 DOI: 10.1038/ki.2014.395] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/02/2014] [Accepted: 10/23/2014] [Indexed: 01/21/2023]
Abstract
Patients tolerant to a kidney graft display a specific blood cell transcriptional pattern but results from five different studies were inconsistent, raising the question of relevance for future clinical application. To resolve this, we sought to identify a common gene signature, specific functional and cellular components, and discriminating biomarkers for tolerance following kidney transplantation. A meta-analysis of studies identified a robust gene signature involving proliferation of B and CD4 T cells, and inhibition of CD14 monocyte related functions among 96 tolerant samples. This signature was further supported through a cross-validation approach, yielding 92.5% accuracy independent of the study of origin. Experimental validation, performed on new tolerant samples and using a selection of the top-20 biomarkers, returned 91.7% of good classification. Beyond the confirmation of B-cell involvement, our data also indicated participation of other cell subsets in tolerance. Thus, the use of the top 20 biomarkers, mostly centered on B cells, may provide a common and standardized tool towards personalized medicine for the monitoring of tolerant or low-risk patients among kidney allotransplant recipients. These data point to a global preservation of genes favoring the maintenance of a homeostatic and ‘healthy' environment in tolerant patients and may contribute to a better understanding of tolerance maintenance mechanisms.
Collapse
|
14
|
Kroksveen AC, Opsahl JA, Guldbrandsen A, Myhr KM, Oveland E, Torkildsen Ø, Berven FS. Cerebrospinal fluid proteomics in multiple sclerosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:746-56. [PMID: 25526888 DOI: 10.1016/j.bbapap.2014.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/27/2014] [Accepted: 12/11/2014] [Indexed: 12/31/2022]
Abstract
Multiple sclerosis (MS) is an immune mediated chronic inflammatory disease of the central nervous system usually initiated during young adulthood, affecting approximately 2.5 million people worldwide. There is currently no cure for MS, but disease modifying treatment has become increasingly more effective, especially when started in the first phase of the disease. The disease course and prognosis are often unpredictable and it can be challenging to determine an early diagnosis. The detection of novel biomarkers to understand more of the disease mechanism, facilitate early diagnosis, predict disease progression, and find treatment targets would be very attractive. Over the last decade there has been an increasing effort toward finding such biomarker candidates. One promising strategy has been to use state-of-the-art quantitative proteomics approaches to compare the cerebrospinal fluid (CSF) proteome between MS and control patients or between different subgroups of MS. In this review we summarize and discuss the status of CSF proteomics in MS, including the latest findings with a focus on the last five years. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Eystein Oveland
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway.
| |
Collapse
|
15
|
Calduch-Giner JA, Echasseriau Y, Crespo D, Baron D, Planas JV, Prunet P, Pérez-Sánchez J. Transcriptional assessment by microarray analysis and large-scale meta-analysis of the metabolic capacity of cardiac and skeletal muscle tissues to cope with reduced nutrient availability in Gilthead Sea Bream (Sparus aurata L.). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:423-435. [PMID: 24626932 DOI: 10.1007/s10126-014-9562-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/06/2014] [Indexed: 06/03/2023]
Abstract
The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart > red skeletal muscle > white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips ( http://fishandchips.genouest.org/index.php ) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species.
Collapse
Affiliation(s)
- Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | | | | | | | | | | |
Collapse
|
16
|
Transcriptional profiling predicts overwhelming homology of schwann cells, olfactory ensheathing cells, and schwann cell-like glia. Glia 2014; 62:1559-81. [DOI: 10.1002/glia.22700] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 01/26/2023]
|
17
|
Ulrich R, Puff C, Wewetzer K, Kalkuhl A, Deschl U, Baumgärtner W. Transcriptional changes in canine distemper virus-induced demyelinating leukoencephalitis favor a biphasic mode of demyelination. PLoS One 2014; 9:e95917. [PMID: 24755553 PMCID: PMC3995819 DOI: 10.1371/journal.pone.0095917] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/01/2014] [Indexed: 01/08/2023] Open
Abstract
Canine distemper virus (CDV)-induced demyelinating leukoencephalitis in dogs (Canis familiaris) is suggested to represent a naturally occurring translational model for subacute sclerosing panencephalitis and multiple sclerosis in humans. The aim of this study was a hypothesis-free microarray analysis of the transcriptional changes within cerebellar specimens of five cases of acute, six cases of subacute demyelinating, and three cases of chronic demyelinating and inflammatory CDV leukoencephalitis as compared to twelve non-infected control dogs. Frozen cerebellar specimens were used for analysis of histopathological changes including demyelination, transcriptional changes employing microarrays, and presence of CDV nucleoprotein RNA and protein using microarrays, RT-qPCR and immunohistochemistry. Microarray analysis revealed 780 differentially expressed probe sets. The dominating change was an up-regulation of genes related to the innate and the humoral immune response, and less distinct the cytotoxic T-cell-mediated immune response in all subtypes of CDV leukoencephalitis as compared to controls. Multiple myelin genes including myelin basic protein and proteolipid protein displayed a selective down-regulation in subacute CDV leukoencephalitis, suggestive of an oligodendrocyte dystrophy. In contrast, a marked up-regulation of multiple immunoglobulin-like expressed sequence tags and the delta polypeptide of the CD3 antigen was observed in chronic CDV leukoencephalitis, in agreement with the hypothesis of an immune-mediated demyelination in the late inflammatory phase of the disease. Analysis of pathways intimately linked to demyelination as determined by morphometry employing correlation-based Gene Set Enrichment Analysis highlighted the pathomechanistic importance of up-regulated genes comprised by the gene ontology terms “viral replication” and “humoral immune response” as well as down-regulated genes functionally related to “metabolite and energy generation”.
Collapse
Affiliation(s)
- Reiner Ulrich
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center of Systems Neuroscience, Hannover, Germany
- * E-mail:
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Konstantin Wewetzer
- Department of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
- Center of Systems Neuroscience, Hannover, Germany
| | - Arno Kalkuhl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riβ), Germany
| | - Ulrich Deschl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riβ), Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center of Systems Neuroscience, Hannover, Germany
| |
Collapse
|
18
|
Raddatz BBR, Hansmann F, Spitzbarth I, Kalkuhl A, Deschl U, Baumgärtner W, Ulrich R. Transcriptomic meta-analysis of multiple sclerosis and its experimental models. PLoS One 2014; 9:e86643. [PMID: 24475162 PMCID: PMC3903571 DOI: 10.1371/journal.pone.0086643] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022] Open
Abstract
Background Multiple microarray analyses of multiple sclerosis (MS) and its experimental models have been published in the last years. Objective Meta-analyses integrate the information from multiple studies and are suggested to be a powerful approach in detecting highly relevant and commonly affected pathways. Data sources ArrayExpress, Gene Expression Omnibus and PubMed databases were screened for microarray gene expression profiling studies of MS and its experimental animal models. Study eligibility criteria Studies comparing central nervous system (CNS) samples of diseased versus healthy individuals with n >1 per group and publically available raw data were selected. Material and Methods Included conditions for re-analysis of differentially expressed genes (DEGs) were MS, myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis (EAE) in rats, proteolipid protein-induced EAE in mice, Theiler’s murine encephalomyelitis virus-induced demyelinating disease (TMEV-IDD), and a transgenic tumor necrosis factor-overexpressing mouse model (TNFtg). Since solely a single MS raw data set fulfilled the inclusion criteria, a merged list containing the DEGs from two MS-studies was additionally included. Cross-study analysis was performed employing list comparisons of DEGs and alternatively Gene Set Enrichment Analysis (GSEA). Results The intersection of DEGs in MS, EAE, TMEV-IDD, and TNFtg contained 12 genes related to macrophage functions. The intersection of EAE, TMEV-IDD and TNFtg comprised 40 DEGs, functionally related to positive regulation of immune response. Over and above, GSEA identified substantially more differentially regulated pathways including coagulation and JAK/STAT-signaling. Conclusion A meta-analysis based on a simple comparison of DEGs is over-conservative. In contrast, the more experimental GSEA approach identified both, a priori anticipated as well as promising new candidate pathways.
Collapse
Affiliation(s)
- Barbara B. R. Raddatz
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ingo Spitzbarth
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Arno Kalkuhl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riß), Germany
| | - Ulrich Deschl
- Department of Non-Clinical Drug Safety, Boehringer Ingelheim Pharma GmbH&Co KG, Biberach (Riß), Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Reiner Ulrich
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
| |
Collapse
|
19
|
Chesneau M, Pallier A, Braza F, Lacombe G, Le Gallou S, Baron D, Giral M, Danger R, Guerif P, Aubert-Wastiaux H, Néel A, Michel L, Laplaud DA, Degauque N, Soulillou JP, Tarte K, Brouard S. Unique B cell differentiation profile in tolerant kidney transplant patients. Am J Transplant 2014; 14:144-55. [PMID: 24354874 DOI: 10.1111/ajt.12508] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 09/11/2013] [Accepted: 09/11/2013] [Indexed: 01/25/2023]
Abstract
Operationally tolerant patients (TOL) display a higher number of blood B cells and transcriptional B cell signature. As they rarely develop an allo-immune response, they could display an abnormal B cell differentiation. We used an in vitro culture system to explore T-dependent differentiation of B cells into plasma cells. B cell phenotype, apoptosis, proliferation, cytokine, immunoglobulin production and markers of differentiation were followed in blood of these patients. Tolerant recipients show a higher frequency of CD20(+) CD24(hi) CD38(hi) transitional and CD20(+) CD38(lo) CD24(lo) naïve B cells compared to patients with stable graft function, correlating with a decreased frequency of CD20(-) CD38(+) CD138(+) differentiated plasma cells, suggestive of abnormal B cell differentiation. B cells from TOL proliferate normally but produce more IL-10. In addition, B cells from tolerant recipients exhibit a defective expression of factors of the end step of differentiation into plasma cells and show a higher propensity for cell death apoptosis compared to patients with stable graft function. This in vitro profile is consistent with down-regulation of B cell differentiation genes and anti-apoptotic B cell genes in these patients in vivo. These data suggest that a balance between B cells producing IL-10 and a deficiency in plasma cells may encourage an environment favorable to the tolerance maintenance.
Collapse
Affiliation(s)
- M Chesneau
- INSERM, UMR 1064, Nantes, France; Faculté de Médecine, Université de Nantes, Nantes, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Obadia T, Sallou O, Ouedraogo M, Guernec G, Lecerf F. The GAG database: A new resource to gather genomic annotation cross-references. Gene X 2013; 527:503-9. [DOI: 10.1016/j.gene.2013.06.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 06/10/2013] [Accepted: 06/19/2013] [Indexed: 11/26/2022] Open
|
21
|
Lasher CD, Rajagopalan P, Murali TM. Summarizing cellular responses as biological process networks. BMC SYSTEMS BIOLOGY 2013; 7:68. [PMID: 23895181 PMCID: PMC3751784 DOI: 10.1186/1752-0509-7-68] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 06/26/2013] [Indexed: 12/02/2022]
Abstract
Background Microarray experiments can simultaneously identify thousands of genes that show significant perturbation in expression between two experimental conditions. Response networks, computed through the integration of gene interaction networks with expression perturbation data, may themselves contain tens of thousands of interactions. Gene set enrichment has become standard for summarizing the results of these analyses in terms functionally coherent collections of genes such as biological processes. However, even these methods can yield hundreds of enriched functions that may overlap considerably. Results We describe a new technique called Markov chain Monte Carlo Biological Process Networks (MCMC-BPN) capable of reporting a highly non-redundant set of links between processes that describe the molecular interactions that are perturbed under a specific biological context. Each link in the BPN represents the perturbed interactions that serve as the interfaces between the two processes connected by the link. We apply MCMC-BPN to publicly available liver-related datasets to demonstrate that the networks formed by the most probable inter-process links reported by MCMC-BPN show high relevance to each biological condition. We show that MCMC-BPN’s ability to discern the few key links from in a very large solution space by comparing results from two other methods for detecting inter-process links. Conclusions MCMC-BPN is successful in using few inter-process links to explain as many of the perturbed gene-gene interactions as possible. Thereby, BPNs summarize the important biological trends within a response network by reporting a digestible number of inter-process links that can be explored in greater detail.
Collapse
Affiliation(s)
- Christopher D Lasher
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA 24061 USA
| | | | | |
Collapse
|
22
|
Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. BMC Bioinformatics 2012; 13:229. [PMID: 22967011 PMCID: PMC3554462 DOI: 10.1186/1471-2105-13-229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categorize and compare these elements using inferred descriptive annotation given this sequence information irrespective of the fact that it may not be representative of the identifier as a whole. RESULTS All annotations, no matter the granularity, can be aligned to genomic sequences and therefore annotated by genomic intervals. We have developed AbsIDconvert, a methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The utility is demonstrated in three case studies: 1) comparative genomic study mapping plasmodium gene sequences to corresponding human and mosquito transcriptional regions; 2) cross-species study of Incyte clone sequences; and 3) analysis of human Ensembl transcripts mapped by Affymetrix®; and Agilent microarray probes. AbsIDconvert currently supports ID conversion of 53 species for a given list of input identifiers, genomic sequence, or genome intervals. CONCLUSION AbsIDconvert provides an efficient and reliable mechanism for conversion between identifier domains of interest. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval. As the genomes and the sequences for genetic elements are further refined, this tool will become increasingly useful and accurate. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bioinformatics.louisville.edu/abid/.
Collapse
Affiliation(s)
- Fahim Mohammad
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA
| | | | | | | | | |
Collapse
|
23
|
Genomic assessment of human cumulus cell marker genes as predictors of oocyte developmental competence: impact of various experimental factors. PLoS One 2012; 7:e40449. [PMID: 22848380 PMCID: PMC3407221 DOI: 10.1371/journal.pone.0040449] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 06/07/2012] [Indexed: 12/01/2022] Open
Abstract
Background Single embryo transfer (SET) is the most successful way to reduce the frequency of multiple pregnancies following in vitro fertilisation. However, selecting the embryo for SET with the highest chances of pregnancy remains a difficult challenge since morphological and kinetics criteria provide poor prediction of both developmental and implantation ability. Partly through the expression of specific genes, the oocyte-cumulus interaction helps the oocyte to acquire its developmental competence. Our aim was therefore to identify at the level of cumulus cells (CCs) genes related to oocyte developmental competence. Methodology/Principal Findings 197 individual CCs were collected from 106 patients undergoing an intra-cytoplasmic sperm injection procedure. Gene expression of CCs was studied using microarray according to the nuclear maturity of the oocyte (immature vs. mature oocyte) and to the developmental competence of the oocyte (ability to reach the blastocyst stage after fertilisation). Microarray study was followed by a meta-analysis of the behaviour of these genes in other datasets available in Gene Expression Omnibus which showed the consistency of this list of genes. Finally, 8 genes were selected according to oocyte developmental competence from the 308 differentially expressed genes (p<0.0001) for further validation by quantitative PCR (qPCR). Three of these 8 selected genes were validated as potential biomarkers (PLIN2, RGS2 and ANG). Experimental factors such as inter-patient and qPCR series variability were then assessed using the Generalised Linear Mixed Model procedure, and only the expression level of RGS2 was confirmed to be related to oocyte developmental competence. The link between biomarkers and pregnancy was finally evaluated and level of RGS2 expression was also correlated with clinical pregnancy. Conclusion/Significance RGS2, known as a regulator of G protein signalling, was the only gene among our 8 selected candidates biomarkers of oocyte competence to cover many factors of variability, including inter-patient factors and experimental conditions.
Collapse
|
24
|
Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet 2012; 13:523-36. [DOI: 10.1038/nrg3253] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
25
|
Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F. GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. Nucleic Acids Res 2012; 40:W458-65. [PMID: 22570409 PMCID: PMC3394256 DOI: 10.1093/nar/gks380] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We present gene prioritization system (GPSy), a cross-species gene prioritization system that facilitates the arduous but critical task of prioritizing genes for follow-up functional analyses. GPSy’s modular design with regard to species, data sets and scoring strategies enables users to formulate queries in a highly flexible manner. Currently, the system encompasses 20 topics related to conserved biological processes including male gamete development discussed in this article. The web server-based tool is freely available at http://gpsy.genouest.org.
Collapse
|
26
|
Klein J, Jupp S, Moulos P, Fernandez M, Buffin‐Meyer B, Casemayou A, Chaaya R, Charonis A, Bascands J, Stevens R, Schanstra JP. The KUPKB: a novel Web application to access multiomics data on kidney disease. FASEB J 2012; 26:2145-53. [DOI: 10.1096/fj.11-194381] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Julie Klein
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Simon Jupp
- School of Computer ScienceUniversity of ManchesterManchesterUK
| | - Panagiotis Moulos
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Myriem Fernandez
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Bénédicte Buffin‐Meyer
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Audrey Casemayou
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Rana Chaaya
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Aristidis Charonis
- Section of HistologyCenter for Basic Research I, Biomedical Research Foundation of the Academy of AthensAthensGreece
| | - Jean‐Loup Bascands
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| | - Robert Stevens
- School of Computer ScienceUniversity of ManchesterManchesterUK
| | - Joost P. Schanstra
- Institut National de la Santé et de la Recherche Médicale, U1048Institut of Cardiovascular and Metabolic DiseaseToulouseFrance
- Université Toulouse III Paul‐SabatierToulouseFrance
| |
Collapse
|
27
|
Prunet P, Øverli Ø, Douxfils J, Bernardini G, Kestemont P, Baron D. Fish welfare and genomics. FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:43-60. [PMID: 21671026 DOI: 10.1007/s10695-011-9522-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 05/31/2011] [Indexed: 05/30/2023]
Abstract
There is a considerable public and scientific debate concerning welfare of fish in aquaculture. In this review, we will consider fish welfare as an integration of physiological, behavioral, and cognitive/emotional responses, all of which are essentially adaptative responses to stressful situations. An overview of fish welfare in this context suggests that understanding will rely on knowledge of all components of allostatic responses to stress and environmental perturbations. The development of genomic technologies provides new approaches to this task, exemplified by how genome-wide analysis of genetic structures and corresponding expression patterns can lead to the discovery of new aspects of adaptative responses. We will illustrate how the genomic approach may give rise to new biomarkers for fish welfare and also increase our understanding of the interaction between physiological, behavioral, and emotional responses. In a first part, we present data on expression of candidate genes selected a priori. This is a common avenue to develop molecular biomarkers capable of diagnosing a stress condition at its earliest onset, in order to allow quick corrective intervention in an aquaculture setting. However, most of these studies address isolated physiological functions and stress responses that may not be truly indicative of animal welfare, and there is only rudimentary understanding of genes related to possible cognitive and emotional responses in fish. We also present an overview on transcriptomic analysis related to the effect of aquaculture stressors, environmental changes (temperature, salinity, hypoxia), or concerning specific behavioral patterns. These studies illustrate the potential of genomic approaches to characterize the complexity of the molecular mechanisms which underlies not only physiological but also behavioral responses in relation to fish welfare. Thirdly, we address proteomic studies on biological responses to stressors such as salinity change and hypoxia. We will also consider proteomic studies developed in mammals in relation to anxiety and depressive status which may lead to new potential candidates in fish. Finally, in the conclusion, we will suggest new developments to facilitate an integrated view of fish welfare. This includes use of laser microdissection in the transcriptomic/proteomic studies, development of meta-analysis methods for extracting information from genomic data sets, and implementation of technological advances for high-throughput proteomic studies. Development of these new approaches should be as productive for our understanding of the biological processes underlying fish welfare as it has been for the progress of pathophysiological research.
Collapse
Affiliation(s)
- P Prunet
- UR1037 SCRIBE, IFR140, INRA, Campus de Beaulieu, Rennes, France.
| | | | | | | | | | | |
Collapse
|
28
|
Baron D, Magot A, Ramstein G, Steenman M, Fayet G, Chevalier C, Jourdon P, Houlgatte R, Savagner F, Pereon Y. Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PLoS One 2011; 6:e26952. [PMID: 22096509 PMCID: PMC3212519 DOI: 10.1371/journal.pone.0026952] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 10/06/2011] [Indexed: 01/12/2023] Open
Abstract
Duchenne Muscular Dystrophy (DMD) is a complex process involving multiple pathways downstream of the primary genetic insult leading to fatal muscle degeneration. Aging muscle is a multifactorial neuromuscular process characterized by impaired muscle regeneration leading to progressive atrophy. We hypothesized that these chronic atrophying situations may share specific myogenic adaptative responses at transcriptional level according to tissue remodeling. Muscle biopsies from four young DMD and four AGED subjects were referred to a group of seven muscle biopsies from young subjects without any neuromuscular disorder and explored through a dedicated expression microarray. We identified 528 differentially expressed genes (out of 2,745 analyzed), of which 328 could be validated by an exhaustive meta-analysis of public microarray datasets referring to DMD and Aging in skeletal muscle. Among the 328 validated co-expressed genes, 50% had the same expression profile in both groups and corresponded to immune/fibrosis responses and mitochondrial metabolism. Generalizing these observed meta-signatures with large compendia of public datasets reinforced our results as they could be also identified in other pathological processes and in diverse physiological conditions. Focusing on the common gene signatures in these two atrophying conditions, we observed enrichment in motifs for candidate transcription factors that may coordinate either the immune/fibrosis responses (ETS1, IRF1, NF1) or the mitochondrial metabolism (ESRRA). Deregulation in their expression could be responsible, at least in part, for the same transcriptome changes initiating the chronic muscle atrophy. This study suggests that distinct pathophysiological processes may share common gene responses and pathways related to specific transcription factors.
Collapse
|
29
|
High-throughput analysis of promoter occupancy reveals new targets for Arx, a gene mutated in mental retardation and interneuronopathies. PLoS One 2011; 6:e25181. [PMID: 21966449 PMCID: PMC3178625 DOI: 10.1371/journal.pone.0025181] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/26/2011] [Indexed: 12/11/2022] Open
Abstract
Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations.
Collapse
|
30
|
Unimodal transform of variables selected by interval segmentation purity for classification tree modeling of high-dimensional microarray data. Talanta 2011; 85:1689-94. [DOI: 10.1016/j.talanta.2011.06.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/28/2011] [Accepted: 06/30/2011] [Indexed: 11/20/2022]
|
31
|
Abstract
BioProfiling.de provides a comprehensive analytical toolkit for the interpretation gene/protein lists. As input, BioProfiling.de accepts a gene/protein list. As output, in one submission, the gene list is analyzed by a collection of tools which employs advanced enrichment or network-based statistical frameworks. The gene list is profiled with respect to the most information available regarding gene function, protein interactions, pathway relationships, in silico predicted microRNA to gene associations, as well as, information collected by text mining. BioProfiling.de provides a user friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. The web portal is freely available at http://www.BioProfiling.de/gene_list.
Collapse
Affiliation(s)
- Alexey V Antonov
- Helmholtz Zentrum München, Institute for Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany.
| |
Collapse
|
32
|
Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R. Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics 2011; 12:113. [PMID: 21324190 PMCID: PMC3049149 DOI: 10.1186/1471-2164-12-113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 02/16/2011] [Indexed: 12/12/2022] Open
Abstract
Background DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc. Description We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (Drosophila melanogaster, Caenorhabditis elegans) and vertebrates (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies. Conclusions Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.
Collapse
|