J Allergy Clin Immunol. 2012 Jan;129(1):88-94.

Interferon regulatory factor 7 is a major hub connecting interferon-mediated responses in virus-induced asthma exacerbations in vivo.

Bosco A, Ehteshami S, Panyala S, Martinez FD.

Arizona Respiratory Center, University of Arizona, Tucson, Ariz, USA. anthonyb@ichr.uwa.edu.au

 

ABSTRACT

BACKGROUND: Exacerbations are responsible for a substantial burden of morbidity and health care use in children with asthma. Most asthma exacerbations are triggered by viral infections; however, the underlying mechanisms have not been systematically investigated.

OBJECTIVE: The objective of this study was to elucidate the molecular networks that underpin virus-induced exacerbations in asthmatic children in vivo.

METHODS: We followed exacerbation-prone asthmatic children prospectively and profiled global patterns of gene expression in nasal lavage samples obtained during an acute, moderate, picornavirus-induced exacerbation and 7 to 14 days later. Coexpression network analysis and prior knowledge was used to reconstruct the underlying gene networks.

RESULTS: The data showed that an intricate modular program consisting of more than 1000 genes was upregulated during acute exacerbations in comparison with 7 to 14 days later. The modules were enriched for coherent cellular processes, including interferon-induced antiviral responses, innate pathogen sensing, response to wounding, small nucleolar RNAs, and the ubiquitin-proteosome and lysosome degradation pathways. Reconstruction of the wiring diagram of the modules revealed the presence of hyperconnected hub nodes, most notably interferon regulatory factor 7, which was identified as a major hub linking interferon-mediated antiviral responses.

CONCLUSIONS: This study provides an integrated view of the inflammatory networks that are upregulated during virus-induced asthma exacerbations in vivo. A series of innate signaling hubs were identified that could be novel therapeutic targets for asthma attacks.

Copyright © 2011 American Academy of Allergy, Asthma & Immunology.

PMID: 22112518

 

Supplement:

Previous immunological and molecular studies pertaining to the role of viruses in asthma have largely focused on a limited number of candidate genes or pathways.  However, this approach is limited, because thousands of genes are differentially expressed during rhinovirus infections in humans.1 Hence, a more complete understanding of the role of viruses in the pathogenesis of asthma will require an approach that can decipher these highly complex biological processes. A significance advance in this context was the application of network graph theory to the analysis of genomic data.2 The underlying concept here is that a functioning biological system can be represented as a network of interconnected nodes and links. The nodes represent genes or their products (e.g. mRNA transcripts, proteins), and the links represent statistical (e.g. mRNA coexpression relationships) or functional (e.g. protein-protein interactions, transcription factor-target gene interactions) relationships between genes. These molecular relationships can be derived from high throughput experiments, and/or extracted from bioinformatics databases or the literature. Seminal work from Barabasi and Albert showed that many complex interconnected systems (e.g. social interaction networks, power grids, the World Wide Web, biological networks) have a “scale-free” network architecture, meaning that the vast majority of nodes are connected to a few other nodes, whereas a few nodes are connected to many nodes, behaving as hubs that dominate the connectivity patterns and essentially “hold” the network together.3 Scale-free networks are tolerant to random perturbations, which would mostly impact on nodes with few connections, but susceptible to the targeted removal of hubs.4 This suggests that hubs which control the activation of inflammatory responses may represent logical therapeutic targets for asthma.5,6 Another fundamental property of biological networks is their organization into smaller, discrete functional units known as modules. Modules comprise sets of densely interconnected genes which function in the same biological pathway or process. Variations in the structure and/or function of modules are thought to underpin diseased states.7,8

In this study we utilized network analysis techniques to characterize the inflammatory mechanisms that are upregulated during virus-induced asthma exacerbations in nasal lavage cells from children. Eight coexpression modules were identified, and they were enriched for coherent biological functions, including but not limited to the interferon mediated antiviral response, innate pathogen sensing, NFkB signalling, regulation of cell death, antigen processing and presentation, chemotaxis, and the protein ubiquitination pathway. Mechanistic data from prior studies was used to reconstruct the wiring diagram of the modules, and this analysis revealed that IRF7 connected the interferon-induced antiviral module and was the dominant hub identified in the study (Fig. 1). STAT1, STAT2, and IRF5 were also hub genes in the antiviral module. NFkB1 and STAT3 were the dominant hubs in the module comprising genes involved in innate pathogen sensing, NFkB signalling, and regulation of cell death.

IRF7 is a transcription factor that activates the expression of type I (interferon-alpha, interferon-beta) and type III interferons (interferon lambda).9,10 IRF7 is constitutively expressed at low levels in the cytoplasm in an inactive state. During viral infections, viral nucleic acids are detected by pathogen recognition receptors of the innate immune system,11,12 and this triggers the phosphorylation and activation of IRF7. IRF7 then translocates to the nucleus to activate expression of the type I interferons. Type I interferon signalling in turn induces more IRF7 transcription, thus forming a positive feedback loop which amplifies the antiviral response. IRF7 is subject to negative regulation by other transcription factors, E3 ubiquitin ligases, and translational repressors.13-16 Type I interferons induce a robust antiviral state in infected and adjacent cells to prevent the spread of infection.17 Type III interferons have similar antiviral properties but primarily function at epithelial surfaces. The central role of IRF7 in the antiviral response has been demonstrated in IRF7 knockout mice, which have deficient interferon responses and succumb to viral infections.9 There is also evidence suggesting that IRF7 can induce an antiviral program independent of type I and III interferon signaling.18

Our data suggests that IRF7 is a major hub for acute asthma, however, the specific function of IRF7 gene networks in asthma exacerbations is unknown. It was reported that interferon-beta and lambda responses to rhinovirus infections in vitro were deficient in primary bronchial epithelial cells from asthmatic subjects in comparison to healthy controls, and this was associated with increased viral loads.19-21 However, asthma exacerbations are associated with specific strains of rhinovirus and additional risk factors (e.g. atopy, natural allergen exposure) which are difficult to model in vitro.22-24 IRF7 expression is upregulated in nasal aspirates from asthmatic children during natural colds.25 Moreover, interferon-alpha and lambda responses were increased during natural rhinovirus infections in respiratory secretions from children with wheeze compared to their nonwheezing counterparts, and levels of interferon lambda were associated with disease severity.26 Interferons and the molecules that regulate their expression may thus play a dual role in asthma. On the one hand, they are a major component of the protective mechanisms against viral infections, and thus, their insufficient activation may contribute to the development of asthma exacerbations, which are predominantly triggered by respiratory viruses. On the other hand, excessive activation of interferon responses may enhance the cascade of inflammatory responses that precipitate such exacerbations.27

Whilst our study has systematically investigated the gene networks that are upregulated in nasal lavage cells during asthma exacerbations, several key questions remain unanswered. We do not know why or how rhinovirus infections trigger asthma exacerbations. Nor do we understand the mechanisms that determine the severity of these illnesses. Follow-up comparative studies of children sampled during natural asthma exacerbations and appropriate control populations without exacerbations should shed further light on these issues.

Fig1Figure 1: IRF7 gene networks are upregulated during virus-induced asthma exacerbations in children. Gene expression levels were compared in nasal lavage cells during the acute exacerbation and at 7-14 days follow-up. Genes connected to IRF7 are shaded blue.

 

Acknowledgements: This study was supported by National Institutes of Health grant HL080083 and the BrightSpark Foundation and McCusker Charitable Foundation.

 

CONTACT:

Anthony Bosco PhD

BrightSpark Foundation McCusker Research Fellow,

Telethon Institute for Child Health Research,

The University of Western Australia.

anthonyb@ichr.uwa.edu.au

 

REFERENCES:

1.         Proud, D., Turner, R.B., Winther, B., Wiehler, S., Tiesman, J.P., et al. Gene expression profiles during in vivo human rhinovirus infection: insights into the host response. Am J Respir Crit Care Med 178, 962-968 (2008).

2.         Barabasi, A.L. & Oltvai, Z.N. Network biology: understanding the cell’s functional organization. Nat Rev Genet 5, 101-113 (2004).

3.         Barabasi, A.L. & Albert, R. Emergence of scaling in random networks. Science 286, 509-512 (1999).

4.         Albert, R., Jeong, H. & Barabasi, A.L. Error and attack tolerance of complex networks. Nature 406, 378-382 (2000).

5.         Bosco, A., McKenna, K.L., Firth, M.J., Sly, P.D. & Holt, P.G. A network modeling approach to analysis of the Th2 memory responses underlying human atopic disease. J Immunol 182, 6011-6021 (2009).

6.         Holt, P.G., Strickland, D.H., Bosco, A. & Jahnsen, F.L. Pathogenic mechanisms of allergic inflammation: atopic asthma as a paradigm. Adv Immunol 104, 51-113 (2009).

7.         Goh, K.I., Cusick, M.E., Valle, D., Childs, B., Vidal, M., et al. The human disease network. Proc Natl Acad Sci U S A 104, 8685-8690 (2007).

8.         Chen, Y., Zhu, J., Lum, P.Y., Yang, X., Pinto, S., et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435 (2008).

9.         Honda, K., Yanai, H., Negishi, H., Asagiri, M., Sato, M., et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772-777 (2005).

10.       Crotta, S., Davidson, S., Mahlakoiv, T., Desmet, C.J., Buckwalter, M.R., et al. Type I and type III interferons drive redundant amplification loops to induce a transcriptional signature in influenza-infected airway epithelia. PLoS Pathog 9, e1003773 (2013).

11.       Chen, Y., Hamati, E., Lee, P.K., Lee, W.M., Wachi, S., et al. Rhinovirus induces airway epithelial gene expression through double-stranded RNA and IFN-dependent pathways. Am J Respir Cell Mol Biol 34, 192-203 (2006).

12.       Wang, Q., Miller, D.J., Bowman, E.R., Nagarkar, D.R., Schneider, D., et al. MDA5 and TLR3 initiate pro-inflammatory signaling pathways leading to rhinovirus-induced airways inflammation and hyperresponsiveness. PLoS Pathog 7, e1002070 (2011).

13.       Colina, R., Costa-Mattioli, M., Dowling, R.J., Jaramillo, M., Tai, L.H., et al. Translational control of the innate immune response through IRF-7. Nature 452, 323-328 (2008).

14.       Yu, Y. & Hayward, G.S. The ubiquitin E3 ligase RAUL negatively regulates type i interferon through ubiquitination of the transcription factors IRF7 and IRF3. Immunity 33, 863-877 (2010).

15.       Litvak, V., Ratushny, A.V., Lampano, A.E., Schmitz, F., Huang, A.C., et al. A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. Nature 490, 421-425 (2012).

16.       Siednienko, J., Jackson, R., Mellett, M., Delagic, N., Yang, S., et al. Pellino3 targets the IRF7 pathway and facilitates autoregulation of TLR3- and viral-induced expression of type I interferons. Nat Immunol 13, 1055-1062 (2012).

17.       Bartlett, N.W., Slater, L., Glanville, N., Haas, J.J., Caramori, G., et al. Defining critical roles for NF-kappaB p65 and type I interferon in innate immunity to rhinovirus. EMBO Mol Med 4, 1244-1260 (2012).

18.       Schmid, S., Mordstein, M., Kochs, G., Garcia-Sastre, A. & Tenoever, B.R. Transcription factor redundancy ensures induction of the antiviral state. J Biol Chem 285, 42013-42022 (2010).

19.       Wark, P.A., Johnston, S.L., Bucchieri, F., Powell, R., Puddicombe, S., et al. Asthmatic bronchial epithelial cells have a deficient innate immune response to infection with rhinovirus. J Exp Med 201, 937-947 (2005).

20.       Contoli, M., Message, S.D., Laza-Stanca, V., Edwards, M.R., Wark, P.A., et al. Role of deficient type III interferon-lambda production in asthma exacerbations. Nat Med 12, 1023-1026 (2006).

21.       Baraldo, S., Contoli, M., Bazzan, E., Turato, G., Padovani, A., et al. Deficient antiviral immune responses in childhood: Distinct roles of atopy and asthma. J Allergy Clin Immunol 130, 1307-1314 (2012).

22.       Bizzintino, J., Lee, W.M., Laing, I.A., Vang, F., Pappas, T., et al. Association between human rhinovirus C and severity of acute asthma in children. Eur Respir J 37, 1037-1042 (2011).

23.       Murray, C.S., Poletti, G., Kebadze, T., Morris, J., Woodcock, A., et al. Study of modifiable risk factors for asthma exacerbations: virus infection and allergen exposure increase the risk of asthma hospital admissions in children. Thorax 61, 376-382 (2006).

24.       Martinez, F.D. Managing childhood asthma: challenge of preventing exacerbations. Pediatrics 123 Suppl 3, S146-150 (2009).

25.       Lewis, T.C., Henderson, T.A., Carpenter, A.R., Ramirez, I.A., McHenry, C.L., et al. Nasal cytokine responses to natural colds in asthmatic children. Clin Exp Allergy 42, 1734-1744 (2012).

26.       Miller, E.K., Hernandez, J.Z., Wimmenauer, V., Shepherd, B.E., Hijano, D., et al. A mechanistic role for type III IFN-lambda1 in asthma exacerbations mediated by human rhinoviruses. Am J Respir Crit Care Med 185, 508-516 (2012).

27.       Holt, P.G. & Sly, P.D. Viral infections and atopy in asthma pathogenesis: new rationales for asthma prevention and treatment. Nat Med 18, 726-735 (2012).

Multiselect Ultimate Query Plugin by InoPlugs Web Design Vienna | Webdesign Wien and Juwelier SchönmannMultiselect Ultimate Query Plugin by InoPlugs Web Design Vienna | Webdesign Wien and Juwelier Schönmann