Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis

Ming Zhao 0 Xiang-dong Liu 0 Xin-yun Li 0 Hong-bo Chen 0 2 Hui Jin 1 Rui Zhou 1 Meng-jin Zhu 0 Shu-hong Zhao 0 0 Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University , Wuhan 430070 , PR China 1 Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070 , PR China 2 School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University , Wuhan 430023Hubei , PR China Background: Network biology (systems biology) approaches are useful tools for elucidating the host infection processes that often accompany complex immune networks. Although many studies have recently focused on Haemophilus parasuis, a model of Gram-negative bacterium, little attention has been paid to the host's immune response to infection. In this article, we use network biology to investigate infection with Haemophilus parasuis in an in vivo pig model. Results: By targeting the spleen immunogenome, we established an expression signature indicative of H. parasuis infection using a PCA/GSEA combined method. We reconstructed the immune network and estimated the network topology parameters that characterize the immunogene expressions in response to H. parasuis infection. The results showed that the immune network of H. parasuis infection is compartmentalized (not globally linked). Statistical analysis revealed that the reconstructed network is scale-free but not small-world. Based on the quantitative topological prioritization, we inferred that the C1R-centered clique might play a vital role in responding to H. parasuis infection. Conclusions: Here, we provide the first report of reconstruction of the immune network in H. parasuis-infected porcine spleen. The distinguishing feature of our work is the focus on utilizing the immunogenome for a network biology-oriented analysis. Our findings complement and extend the frontiers of knowledge of host infection biology for H. parasuis and also provide a new clue for systems infection biology of Gram-negative bacilli in mammals. - Background Glsser's disease is caused by Haemophilus parasuis (shortened as H. parasuis or HPS), a model Gramnegative bacillus. This disease is an important cause of economic loss in the world's pig industry, which is clinically characterized by fibrinous polyserositis, polyarthritis and meningitis [1]. To date, the major focus of studies of porcine Glsser's disease has centered on clinical symptoms, pathology and diagnosis, susceptibility and epidemiology, pathogenic biology, vaccine development, and evaluation of virulence-associated factors [2-6]. Many of these investigations have highly focused on the major aspects of biology and pathogenesis for the H. parasuis bacterium itself. Aside from several recent studies [7-11], the molecular mechanisms of the pig host that are involved in the response to the H. parasuis invasion have not been well addressed. More importantly, the pig is an excellent biomedical model because it has a closer phylogenetic and physiological relationship to humans than rodent models [12]. In addition to being a potential asset for undiscovered clinical and therapeutic needs, pigs infected with H. parasuis could also serve as mammalian and human models for bacterial infectious diseases. It is well known that the immune genes (hereafter referred to as immunogenes) have played central roles in the regulation of pathogen-induced host processes in vivo, including those of Glsser's disease. Systems biology (also referred to as network biology) approaches have brought a research paradigm for infectious diseases; for example, a systems biology program was recently initiated by the National Institute of Allergy and Infectious Diseases [13]. Systems biology investigations of the transcriptome of host immunogenome could provide a profound exploration of the molecular events occurring, for example, the three- or even four-dimensional relationships between genes during a response to pathogen infection. This would increase our understanding of host resistance/susceptibility genes, immune response mechanisms, and molecular basis of hostpathogen interactions [14,15]. So, the systems biology approaches can also provide us with powerful tools for uncovering the molecular immune mechanisms that defend against H. parasuis infection. Custom-build gene chips have been widely applied in a variety of investigations [16-21]. On many occasions, a reduced fragment of microarray data could work more efficiently to reveal more subtle insights into the target biological phenomena than the non-reduced global genome data do [22-24]. As a consequence, an analysis focusing on immunogenes could give a more precise exploration of the transcriptomic landscape of infectioninduced immune processes in hosts. In the body's immune system, spleen is an important target organ for studies of immune mechanisms. It has been well documented that the spleen is a crucial immune organ to protect the body against a variety of diseases and infections [25-27]. The spleen, known as the blood cleaner for its role in capturing foreign antigens and destroying old red blood cells, is made up of a variety of immune cells and blood cells, including B cells, T cells, macrophages, dendritic cells, natural killer cells and red blood cells [28-31]. When migratory macrophages and dendritic cells bring antigens to the spleen, the immune cells (e.g., T- and B-lymphocytes) become activated and trigger a series of immune responses [32-35]. Although not obligatory for survival, it has been proven that the spleen plays a key role in mounting immune responses to antigens, and in the absence of the spleen, the body would be more susceptible to infections [36]. Consequently, the spleen is one of the ideal organ models for studying host immune responses to pathogenic challenges, including the H. parasuis infection. Our previous study has used the Affymetrix Porcine Genechip to profile the differentially expressed genes between spleens with and without administrations with the H. parasuis [10]. There were totally 931 differentially expressed transcripts, of which only a small fragment has been annotated as immunogenes. The result showed that the unfocused global expression profiling based on a full-genome array couldnt reveal the subtle roles of immunogenes. In the present study, we aim to clarify the subtle roles of immunogenes in the host response to H. parasuis challenge. Using the pig (Sus scrofa) as an in vivo model, we first characterized the microarray expression dataset of the spleen's immunogenome. Based on the partitioned immunogenome dataset, we performed a comprehensive immunomic analysis, which included reconstruction of the immune network and evaluation of network parameters and quantitative topological properties. Our investigation revealed a vital network component in response to H. parasuis infection. T (...truncated)