Network analysis of human glaucomatous optic nerve head astrocytes

BMC Medical Genomics BioMed Central Research article Open Access Network analysis of human glaucomatous optic nerve head astrocytes Tatiana Nikolskaya†1, Yuri Nikolsky†2, Tatiana Serebryiskaya1, Svetlana Zvereva1, Eugene Sviridov1, Zoltan Dezso2, Eugene Rahkmatulin2, Richard J Brennan2, Nick Yankovsky1, Sanjoy K Bhattacharya3,4, Olga Agapova5, M Rosario Hernandez6 and Valery I Shestopalov*3,7 Address: 1Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str, Moscow, Russia, 2GeneGo Inc, 500 Renaissance Drive, Suite 106, St. Joseph, MI, 49085, USA, 3Current address: Bascom Palmer Eye Institute Department of Ophthalmology, University of Miami Miller School of Medicine; 1638 NW 10th Avenue, Miami, FL 33136, USA, 4Department of Molecular Biology and Biochemistry, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA, 5Department of Ophthalmology and Visual Sciences Washington University School of Medicine 660 South Euclid Ave, St Louis, MO 63110, USA, 6Department of Ophthalmology, Feinberg School of Medicine, Northwestern University Chicago, IL 60611, USA and 7Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA Email: Tatiana Nikolskaya - ; Yuri Nikolsky - ; Tatiana Serebryiskaya - ; Svetlana Zvereva - ; Eugene Sviridov - ; Zoltan Dezso - ; Eugene Rahkmatulin - ; Richard J Brennan - ; Nick Yankovsky - ; Sanjoy K Bhattacharya - ; Olga Agapova - ; M Rosario Hernandez - ; Valery I Shestopalov* - * Corresponding author †Equal contributors Published: 9 May 2009 BMC Medical Genomics 2009, 2:24 doi:10.1186/1755-8794-2-24 Received: 25 April 2008 Accepted: 9 May 2009 This article is available from: http://www.biomedcentral.com/1755-8794/2/24 © 2009 Nikolskaya et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Astrocyte activation is a characteristic response to injury in the central nervous system, and can be either neurotoxic or neuroprotective, while the regulation of both roles remains elusive. Methods: To decipher the regulatory elements controlling astrocyte-mediated neurotoxicity in glaucoma, we conducted a systems-level functional analysis of gene expression, proteomic and genetic data associated with reactive optic nerve head astrocytes (ONHAs). Results: Our reconstruction of the molecular interactions affected by glaucoma revealed multi-domain biological networks controlling activation of ONHAs at the level of intercellular stimuli, intracellular signaling and core effectors. The analysis revealed that synergistic action of the transcription factors AP1, vitamin D receptor and Nuclear Factor-kappaB in cross-activation of multiple pathways, including inflammatory cytokines, complement, clusterin, ephrins, and multiple metabolic pathways. We found that the products of over two thirds of genes linked to glaucoma by genetic analysis can be functionally interconnected into one epistatic network via experimentally-validated interactions. Finally, we built and analyzed an integrative disease pathology network from a combined set of genes revealed in genetic studies, genes differentially expressed in glaucoma and closely connected genes/proteins in the interactome. Conclusion: Our results suggest several key biological network modules that are involved in regulating neurotoxicity of reactive astrocytes in glaucoma, and comprise potential targets for cell-based therapy. Page 1 of 26 (page number not for citation purposes) BMC Medical Genomics 2009, 2:24 Background Astrocyte activation is a hallmark of various CNS injuries and pathologies, including stroke, trauma, tumor, infection, and neurodegenerative diseases [1-3]. Upon activation, astrocytes display altered metabolism and the ability to preserve CNS homeostasis and support neuronal function. Reactive astrocytes were shown to reduce damage during the acute phase of CNS insults [4]. In contrast, progressive degenerative diseases, such as glaucoma, feature chronic astrocyte activation that exacerbates damage to neurons and impairs regeneration of their axons [5,6]. Importantly, a prominent astrocyte reactivation in primary open angle glaucoma (POAG) is localized to the optic nerve head, which is also the site of primary damage to the retinal ganglion cells (RGCs) [7]. In common with many other complex, age-related diseases, neurodegeneration in POAG is associated with a homeostatic imbalance resulting from environmental factors and multiple genetic components interconnected within complex epistatic networks [8]. Such imbalance is manifested at three interconnected functional levels: intercellular stimuli, intracellular signal transduction, and core effectors (i.e. endogenous metabolism, structural complexes, etc). Disease causes alterations at all three levels. These can be measured by high-content screens that include differential gene expression, proteomics and metabolomics, as well as in genetic linkage studies that connect genes or protein variants to disease onset [9,10]. Recent progress in systems biology has allowed a quantification, cross-comparison and functional interpretation of heterogeneous datasets within the framework of human biological pathways, networks and processes, which are assembled from a knowledgebase of functional biological interactions [10,11]. This systems level approach requires an understanding of connectivity between the genes and proteins affected in a given disease. Connectivity is defined by binary protein interactions with genes, proteins and biologically active compounds [12]. The biological networks are scale-free but converge in regulatory nodes and modules, such as major transcription factors and receptors [13,14]. Identification of such key topological elements [15,16] on the networks derived from disease-related data may reveal potential therapeutic targets. This approach is particularly powerful for diseases of complex etiology, such as glaucoma. Regulation of astrocyte activation, which is associated with increased neurotoxicity, involves differential activation of key cellular network modules [17]. To perform in silico reconstructions of the cellular pathways affected during the development of glaucoma, however, data derived specifically from astrocytes must be used, rather than data derived from whole-tissue (retina or optic nerve) samples. It is feasible to suggest that the cell-specific data from http://www.biomedcentral.com/1755-8794/2/24 interacting cell types, such as astrocytes and retinal ganglion cells, will allow us to analyze differences in trans-cellular crosstalk that are implicated in glaucoma. Here, we performed functional analysis of the signal (...truncated)