Prediction Of MiRNA-regulated Double-colour Networks Of PPIS In Pigs And Investigation On Systems Biology Of Evolutional Network Of Molecules Involved In Pathogenesis And Immune Mechanism Of Respiratory Virosis

Protein-protein interaction (PPI) is one of the most important function components ofcell. Nowadays, scientists pay special attention to the double-colour network of miRNAregulation of PPIs, which not only helps to understand the miRNA fine-tuning role in PPInetworks, but also provides scientific basis for epidemic disease prevention. Highlypathogenic porcine reproductive and respiratory syndrome (HP-PRRS) and Swine influenza(SI) caused severe damage in the global swine industry. In this study, we predicted the PPInetworks of pigs and constructed the double colour network involving miRNA regulation ofPPI of pig. We studied the molecular mechanism regarding systems biology of pigletsinfected with HP-PRRSV or SIV(H1N1), which provides reference to understand thebiological processes. The main contents of the paper are summarized as follows:(1) We used three methods, Interolog-based prediction of porcine PPI network (PPIN),domain-motif interactions from structural topology-based prediction of porcine PPI networkand motif-motif interactions from structural topology-based prediction of porcine PPInetwork, to predict porcine protein interactions among25,767porcine proteins. We predicted20,213,331,484, and218,705porcine PPIs respectively, merged the three results into567,441PPIs, constructed four PPI networks and analyzed the topological properties of theporcine PPI networks. Our predictions were validated with Pfam domain annotations and GOannotations. Averages of70,10,495, and863interactions were related to the Pfamdomain-interacting pairs in iPfam database. For comparison, randomized networks weregenerated, and averages of only4.24,66.79, and44.26interactions were associated withPfam domain-interacting pairs in iPfam database. In GO annotations, we found52.68%,75.54%,27.20%of the predicted PPIs sharing GO terms respectively. However, the numberof PPI pairs sharing GO terms in the10,000randomized networks reached52.68%,75.54%,27.20%is0. Finally, we determined the accuracy and precision of the methods. The methods yielded accuracies of0.92,0.53, and0.50and precisions of about0.93,0.74, and0.75,respectively. The results reveal that the predicted PPI networks are considerably reliable. Wealso constructed a website (http://pppid.songbx.me/) for sharing porcine PPIs, at which theporcine PPI data set, the confidence score of each interaction and a list of related data wereall available. Finally, we analyzed differentially expressed proteins and proteinphosphorylation data obtained by our group in piglets infected with highly pathogenicporcine reproductive and respiratory syndrome virus (HP-PRRSV) in the PPI network webuilt, and found key proteins that may be involved in the process of highly pathogenicporcine reproductive and respiratory syndrome (HP-PRRS), including Q6QA25(Tropomyosin alpha-3chain), Q29214(60S acidic ribosomal protein P0), Q31068(MHCPD14transplantation antigen), Q2XQY5(Tropomyosin3), Q8SPS7(Haptoglobin), Q69DK8(Complement C1s subcomponet) and P01965(Hemoglobin subunit alpha), which thus can beused as therapy targets. We also found that biological processes such as hormone, injuryreaction, response to temperature stimulation, the respiratory system development,inflammation reaction may play a key role in clarifying the pathogenesis of HP-PRRS usingGO enrichment analysis.(2) Double-colour network including miRNA regulation of pig PPIN was constructed forthe first time, and282867miRNA-regulated swine PPIs were obtained. Pathways from thewhole network were analyzed and some pathway-pathway interactions were found. Inaddition,2457miRNA-regulated disease-related PPIs were predicted using Interolog method.100disease-associated miRNA got through literature mining were mapped into thedouble-color network, and2040miRNA-regulated disease-related PPIs were obtained,showing that the predicted result was rather reliable. The GO enrichment analysis of these2040miRNA-regulated disease-related PPIs showed that their functions were mainlystimulus response, oncogenesis, inflammatory response et al., certifying that these proteinswere associated with disease. Thus, miRNA-regulated disease-related PPIN provides a goodperspective for diagnosis, prevention, treatment and drug development. Finally, thedifferentially expressed proteins of lungs, mandibular lymph nodes and serum of pigletsinfected with HP-PRRSV, which were measured by our group before, were analyzed usingthe miRNA-regulated double-colour network of PPIs we constructed to discover the proteinsand miRNAs which could be targets for treatment of HP-PRRS, proteins including B8XSI6(Phosphatase and tesin-like protein), P01965(Hemoglobin subunit alpha), P20305(Gelsolin),Q31068(MHC PD14transplantation antigen), Q6QAQ1(Actin, cytoplasmic1), A1XSY8(E3, SUMO-protein ligase EGR2) and miRNAs including ssc-miR-145-3p, ssc-miR-30a-5p,ssc-miR-30b-5p, ssc-miR-30c-5p, ssc-let-7a, ssc-let-7c, ssc-let-7d-5p, ssc-let-7e, ssc-let-7f, ssc-let-7g, ssc-let-7i, ssc-miR-181c, ssc-miR-182and ssc-miR-23a.(3) The molecular mechanism regarding systems biology of HP-PRRSV and SIV(H1N1)infection of piglet was analyzed. Networks involved in differential miRNAs and proteinsidentified by our group from the submandibular lymph nodes, lung, and serum, and proteinphosphorylation of piglets infected with HP-PRRSV and H1N1were extracted from porcinePPIN and miRNA-regulated PPIN earlier. Through analyzing the networks, we founddifferential proteins B8XSI6(Phosphatase and tesin-like protein), Q2XQY5(Tropomyosin3),B5APU3(Actin-related protein2-like protein), Q31068(MHC PD14transplantation antigen),Q29214(60S acidic ribosomal protein P0), P09571(Serotransferrin), Q04967(Heat shock70kDa protein6), Q6QA25(Tropomyosin alpha-3chain), P01965(Hemoglobin subunitalpha), B5APU8(Actin related protein2/3complex subunit3), P20305(Gelsolin), Q69DK8(Complement C1s subcomponet), Q8SPS7(Haptoglobin), Q9GMA7(Alpha-1-antichymotrypsin1), and phosphorylated protein P15981(SLA classâ…¡histocompatibility antigen, DQ haplotype D alpha chain), Q4AC39(MHC class I antigen),Q547Q5(MHC classâ…¡ antigen), Q19LF1(Nuclear receptor corepressor2), Q32YV9(Proteasome26S subunit non-ATPase4) and Q29214(60S acidic ribosomal protein P0) maybe used as drug targets for HP-PRRS treatment in the process of HP-PRRSV infection ofpiglets. MiRNAs containing ssc-miR-15a, ssc-miR-15b, ssc-miR-16, ssc-miR-195,ssc-miR-30a-5p, ssc-30b-5p, ssc-miR-30c-5p, ssc-miR-181c, ssc-miR-20a, ssc-miR-20b,ssc-miR-32, ssc-miR-153and ssc-miR-145-3p and seven modules of miRNA-coordinatedproteins play an important role in the pathogenesis of HP-PRRS. Phosphorylated proteinB6CVD6(Thioredoxin domain-containing4) regulated by11miRNA was identified inmiRNA regulation of differential phosphorylated protein network, which was speculated tobe an important factor of HP-PRRS occurrence. And we also identified that the differentialPPI regulated by differently expressed miRNAs among DPI0, DPI4and DPI7were mainlyinvolved in immune responses, hormone response, breeding, courtship and mating behaviorand so on, providing theoretical basis for understanding the molecular pathogenesis ofsystems biology of respiratory virosis of piglets.