Genome-wide Gene Expression Analysis in the Amphioxus, After Poly (I: C) Challenge Using Strand-specific RNA-seq

Overview

Journal Oncotarget

Specialty Oncology

Date 2018 Jan 10

PMID 29312538

Authors

Qi-Lin Zhang

Zheng-Qing Xie

Ming-Zhong Liang

Bang Luo

Xiu-Qiang Wang

Jun-Yuan Chen

Affiliations

Soon will be listed here.

Abstract

The gene expression associated with immune response to bacteria/bacterial mimic has been extensively analyzed in amphioxus, but remains largely unknown about how gene are involved in the immune response to viral invasion at expression level. Here, we analyze the rRNA-depleted transcriptomes of using strand-specific RNA-seq in response to the viral mimic, poly (I:C) (pIC). A total of 5,317 differentially expressed genes were detected at treatment group by comparing with control. The gene with the most significant expression changes (top 15) after pIC challenge and 7 immune-related categories involving 58 differently expressed genes were scrutinized. By functional enrichment analysis of differently expressed genes, gene ontology terms involving response to stress and stimulus, apoptosis, catabolic and metabolic processes and enzyme activity were overrepresented, and several pathways related to immune signaling, immune response, cancer, apoptosis, viral disease, metabolism were activated after pIC injection. A positive correlation between the qRT-PCR and strand-specific RNA-seq data confirmed the accuracy of the RNA-seq results. Additionally, the expression of genes encoding NLRC5, CASP1, CASP6, CYP450, CAT, and MDA5 were induced in under pIC challenge. Our experiments provide insight into the immune response of amphioxus to pIC and valuable gene expression information for studying the evolution of antiviral immunity in vertebrates.

References

Wang Y, Zhang S . EF1α is a useful internal reference for studies of gene expression regulation in amphioxus Branchiostoma japonicum. Fish Shellfish Immunol. 2012; 32(6):1068-73. DOI: 10.1016/j.fsi.2012.03.001. View

Liebscher I, Schon J, Petersen S, Fischer L, Auerbach N, Demberg L . A tethered agonist within the ectodomain activates the adhesion G protein-coupled receptors GPR126 and GPR133. Cell Rep. 2014; 9(6):2018-26. PMC: 4277498. DOI: 10.1016/j.celrep.2014.11.036. View

Wang S, Chen Y, Wu Q, Hua Z . Detection of Fas-associated death domain and its variants' self-association by fluorescence resonance energy transfer in living cells. Mol Imaging. 2013; 12(2):111-20. View

Lei M, Liu H, Liu S, Zhang Y, Zhang S . Identification and functional characterization of viperin of amphioxus Branchiostoma japonicum: Implications for ancient origin of viperin-mediated antiviral response. Dev Comp Immunol. 2015; 53(2):293-302. DOI: 10.1016/j.dci.2015.07.008. View

Du C, Zhang Q, Li C, Miao D, Gui J . Induction of apoptosis in a carp leucocyte cell line infected with turbot (Scophthalmus maximus L.) rhabdovirus. Virus Res. 2004; 101(2):119-26. DOI: 10.1016/j.virusres.2003.12.034. View

Cui J, Zhu L, Xia X, Wang H, Legras X, Hong J . NLRC5 negatively regulates the NF-kappaB and type I interferon signaling pathways. Cell. 2010; 141(3):483-96. PMC: 3150216. DOI: 10.1016/j.cell.2010.03.040. View

Vince J, Silke J . The intersection of cell death and inflammasome activation. Cell Mol Life Sci. 2016; 73(11-12):2349-67. PMC: 11108284. DOI: 10.1007/s00018-016-2205-2. View

Liu Z, Li L, Li H, Zhang S, Ji G, Sun Y . EST analysis of the immune-relevant genes in Chinese amphioxus challenged with lipopolysaccharide. Fish Shellfish Immunol. 2009; 26(6):843-9. DOI: 10.1016/j.fsi.2009.03.017. View

Yang J, He J, Cao H, Zhao X, Fu S, Lu H . Correlation between plasma amino acid profiles and the various stages of hepatitis B infection. Eur J Clin Microbiol Infect Dis. 2012; 31(8):2045-52. DOI: 10.1007/s10096-011-1538-x. View

10.

Yuan S, Yu Y, Huang S, Liu T, Wu T, Dong M . Bbt-TNFR1 and Bbt-TNFR2, two tumor necrosis factor receptors from Chinese amphioxus involve in host defense. Mol Immunol. 2006; 44(5):756-62. DOI: 10.1016/j.molimm.2006.04.011. View

11.

Chien S, Reiter L, Bier E, Gribskov M . Homophila: human disease gene cognates in Drosophila. Nucleic Acids Res. 2001; 30(1):149-51. PMC: 99119. DOI: 10.1093/nar/30.1.149. View

12.

Chen J, Lu X, Yang H, Shi Y . An interaction between a C-type lectin receptor and leukocyte cell-derived chemotaxin 2 of ayu, Plecoglossus altivelis. Fish Shellfish Immunol. 2009; 28(1):245-8. DOI: 10.1016/j.fsi.2009.10.011. View

13.

Kimura T, Takanami T, Sakashita T, Wada S, Kobayashi Y, Higashitani A . Innate immune genes including a mucin-like gene, mul-1, induced by ionizing radiation in Caenorhabditis elegans. Radiat Res. 2012; 178(4):313-20. DOI: 10.1667/rr2989.1. View

14.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

15.

Weake V, Workman J . Histone ubiquitination: triggering gene activity. Mol Cell. 2008; 29(6):653-63. DOI: 10.1016/j.molcel.2008.02.014. View

16.

Li S, Tighe S, Nicolet C, Grove D, Levy S, Farmerie W . Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol. 2014; 32(9):915-925. PMC: 4167418. DOI: 10.1038/nbt.2972. View

17.

Satoh T, Kato H, Kumagai Y, Yoneyama M, Sato S, Matsushita K . LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses. Proc Natl Acad Sci U S A. 2010; 107(4):1512-7. PMC: 2824407. DOI: 10.1073/pnas.0912986107. View

18.

Li D, Li G, Wang K, Liu X, Li W, Chen X . Isolation and functional analysis of the promoter of the amphioxus Hsp70a gene. Gene. 2012; 510(1):39-46. DOI: 10.1016/j.gene.2012.08.031. View

19.

Ryzhakov G, Lai C, Blazek K, To K, Hussell T, Udalova I . IL-17 boosts proinflammatory outcome of antiviral response in human cells. J Immunol. 2011; 187(10):5357-62. DOI: 10.4049/jimmunol.1100917. View

20.

Huang S, Chen Z, Yan X, Yu T, Huang G, Yan Q . Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun. 2014; 5:5896. PMC: 4284660. DOI: 10.1038/ncomms6896. View