Combining of transcriptomic and proteomic data to mine immune-related genes and proteins in the liver of Cynoglossus semilaevis challenged with Vibrio anguillarum

Ackerman, 2004, Cellular mechanisms governing cross-presentation of exogenous antigens, Nat. Immunol., 5, 678, 10.1038/ni1082 Anders, 2015, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638 Andersen, 2004, Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets, Cancer Res., 64, 5245, 10.1158/0008-5472.CAN-04-0496 Barbe, 2014, Advances in Nod-like receptors (NLR) biology, Cytokine Growth Factor Rev., 25, 681, 10.1016/j.cytogfr.2014.07.001 Bergström, 2015, Antigen-induced regulation of T-cell motility, interaction with antigen-presenting cells and activation through endogenous thrombospondin-1 and its receptors, Immunol, 144, 687, 10.1111/imm.12424 Bertolino, 2002, Role of primary intrahepatic T-cell activation in the ‘liver tolerance effect’, Immunol. Cell Biol., 80, 84, 10.1046/j.0818-9641.2001.01048.x Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Boraschi, 2018, The family of the interleukin-1 receptors, Immunol. Rev., 281, 197, 10.1111/imr.12606 Chen, 2010, Molecular characterization and expression analysis of nuclear oligomerization domain proteins NOD1 and NOD2 in grass carp Ctenopharyngodon idella, Fish Shellfish Immunol., 28, 18, 10.1016/j.fsi.2009.09.012 Chen, 2014, Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle, Nat. Genet., 46, 253, 10.1038/ng.2890 Dietrich, 2019, Proteomic and metabolomic insights into the functions of the male reproductive system in fishes, Theriogenology, 132, 182, 10.1016/j.theriogenology.2019.04.018 Fei, 2020, Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during cyprinid herpesvirus 2 infection in vitro, Fish Shellfish Immunol., 106, 167, 10.1016/j.fsi.2020.07.044 Franceschini, 2012, STRING v9.1: protein-protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 41, 808, 10.1093/nar/gks1094 Gonzalez, 2007, Complement expression in common carp (Cyprinus carpio L.) during infection with Ichthyophthirius multifiliis, Dev. Comp. Immunol., 31, 576, 10.1016/j.dci.2006.08.010 Hayashi, 2001, The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5, Nature, 410, 1099, 10.1038/35074106 Ilienko, 2016, Overexpression of TP53, TP53I3 and BIRC5, alterations of gene regulation of apoptosis and aging of human immune cells in a remote period after radiation exposure, Probl. Radiac. Med. Radiobiol., 21, 238, 10.33145/2304-8336-2016-21-238-246 Jean Beltran, 2017, Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases, Mol. Syst. Biol., 13, 922, 10.15252/msb.20167062 Kanehisa, 2007, KEGG for linking genomes to life and the environment, Nucleic Acids Res., 36, 480, 10.1093/nar/gkm882 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Koul, 2013, Role of p38 MAP kinase signal transduction in solid tumors, Genes Cancer, 4, 342, 10.1177/1947601913507951 Laing, 2008, A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish, BMC Evol. Biol., 8, 42, 10.1186/1471-2148-8-42 Li, 2019, Curcumin inhibits cigarette smoke-induced inflammation via modulating the PPARγ-NF-κB signaling pathway, Food Funct., 10, 7983, 10.1039/C9FO02159K Li, 2020, Integrated transcriptomic and proteomic analyses of grass carp intestines after vaccination with a double-targeted DNA vaccine of Vibrio mimicus, Fish Shellfish Immunol., 98, 641, 10.1016/j.fsi.2019.10.045 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT Method, Methods, 25, 402, 10.1006/meth.2001.1262 Lu, 2014, iTRAQ analysis of gill proteins from the zebrafish (Danio rerio) infected with Aeromonas hydrophila, Fish Shellfish Immunol., 36, 229, 10.1016/j.fsi.2013.11.007 Luo, 2019, Integrated dual RNA-seq and dual iTRAQ of infected tissue reveals the functions of a diguanylate cyclase gene of Pseudomonas plecoglossicida in host-pathogen interactions with Epinephelus coioides, Fish Shellfish Immunol., 95, 481, 10.1016/j.fsi.2019.11.008 Mohamad, 2019, Vibriosis in cultured marine fishes: a review, Aquaculture, 512, 10.1016/j.aquaculture.2019.734289 Narizhneva, 2005, Thrombospondin-1 up-regulates expression of cell adhesion molecules and promotes monocyte binding to endothelium, FASEB J., 19, 1158, 10.1096/fj.04-3310fje Oura, 2011, Extracellular heat shock protein 90 plays a role in translocating chaperoned antigen from endosome to proteasome for generating antigenic peptide to be cross-presented by dendritic cells, Int. Immunol., 23, 223, 10.1093/intimm/dxq475 Peters, 2013, IL-1 receptor 2 (IL-1R2) and its role in immune regulation, Brain Behav. Immun., 32, 1, 10.1016/j.bbi.2012.11.006 Pontigo, 2016, Identification and expressional analysis of NLRC5 inflammasome gene in smolting Atlantic salmon (Salmo salar), Fish Shellfish Immunol., 58, 259, 10.1016/j.fsi.2016.09.031 Qin, 2006, The complement system in liver diseases, Cell. Mol. Immunol., 3, 333 Racanelli, 2006, The liver as an immunological organ, Hepatology, 43, S54, 10.1002/hep.21060 Raida, 2009, Innate immune response in rainbow trout (Oncorhynchus mykiss) against primary and secondary infections with Yersinia ruckeri O1, Dev. Comp. Immunol., 33, 35, 10.1016/j.dci.2008.07.001 Secombes, 1997, Host-pathogen interactions in salmonids, 269 Seki, 2008, Toll-like receptors and adaptor molecules in liver disease: update, Hepatology, 48, 322, 10.1002/hep.22306 Sha, 2009, NOD-like subfamily of the nucleotide-binding domain and leucine-rich repeat containing family receptors and their expression in channel catfish, Dev. Comp. Immunol., 33, 991, 10.1016/j.dci.2009.04.004 Sha, 2010, Generation and analysis of 10 000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers, J. Fish Biol., 76, 1190, 10.1111/j.1095-8649.2010.02592.x Smith, 1985, Measurement of protein using bicinchoninic acid, Anal. Biochem., 150, 76, 10.1016/0003-2697(85)90442-7 Smoot, 2011, Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, 27, 431, 10.1093/bioinformatics/btq675 Sun, 2018, Integration of RNAi and RNA-seq reveals the immune responses of Epinephelus coioides to sigX gene of Pseudomonas plecoglossicida, Front. Immunol., 9, 1624, 10.3389/fimmu.2018.01624 Tang, 2008, Isolation and characterization of pathogenic Listonella anguillarum of diseased half-smooth tongue sole (Cynoglossus semilaevis Günther), J. Ocean Univ. China, 7, 343, 10.1007/s11802-008-0343-3 Tjelle, 2000, Phagosome dynamics and function, Bioessays, 22, 255, 10.1002/(SICI)1521-1878(200003)22:3<255::AID-BIES7>3.0.CO;2-R Trapnell, 2010, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621 Vandesompele, 2002, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol., 3, 00341, 10.1186/gb-2002-3-7-research0034 Wang, 2019, Transcriptome comparative analysis of immune tissues from asymptomatic and diseased Epinephelus moara naturally infected with nervous necrosis virus, Fish Shellfish Immunol., 93, 99, 10.1016/j.fsi.2019.07.020 Wang, 2019, Transcriptome analysis in the skin of Carassius auratus challenged with Aeromonas hydrophila, Fish Shellfish Immunol., 94, 510, 10.1016/j.fsi.2019.09.039 Westermann, 2012, Dual RNA-seq of pathogen and host, Nat. Rev. Microbiol., 10, 618, 10.1038/nrmicro2852 Wisniewski, 2009, Universal sample preparation method for proteome analysis, Nat. Methods, 6, 359, 10.1038/nmeth.1322 Yuan, 2019, Puerarin protects pulmonary arteries from hypoxic injury through the BMPRII and PPARγ signaling pathways in endothelial cells, Pharmacol. Rep., 71, 855, 10.1016/j.pharep.2019.05.002 Zeng, 2015, sghC1q, a novel C1q family member from half-smooth tongue sole (Cynoglossus semilaevis): identification, expression and analysis of antibacterial and antiviral activities, Dev. Comp. Immunol., 48, 151, 10.1016/j.dci.2014.09.010 Zhang, 2010, The role of apolipoprotein E in Guillain-Barré syndrome and experimental autoimmune neuritis, J. Biomed. Biotechnol., 2010, 357, 10.1155/2010/357412 Zhang, 2015, Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection, Fish Shellfish Immunol., 43, 209, 10.1016/j.fsi.2014.11.018 Zhang, 2018, Nucleotide-binding and oligomerization domain (NOD)-like receptors in teleost fish: current knowledge and future perspectives, J. Fish Dis., 41, 1317, 10.1111/jfd.12841 Zhang, 2021, TMT-based quantitative proteomic analysis of hepatic tissue reveals the effects of dietary cyanidin-3-diglucoside-5-glucoside-rich extract on alleviating D-galactose-induced aging in mice, J. Proteome, 232, 10.1016/j.jprot.2020.104042