Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain.

Zhiying Jia,Xiao-Qin Xia,Chitao Li,Weidong Ye,Yingyin Cheng,Xiaona Jiang,Nan Wu,Mijuan Shi,Junwei Shan,Xuesong Hu,Jiaxin Sun,Heng Li,Yanlong Ge,Ying Tang,Lianyu Shi

doi:10.3389/fimmu.2021.687151

Abstract

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp developed resistance to CyHV-3 infection. This study illustrates the immune mechanisms involved in both sensitivity and anti-virus ability for CyHV3 infection in fish. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at days 0 (the healthy control) and 7 after CyHV-3 infection (the survivors) and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. To dig out details on the immune aspect, the DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops a marked resistance to CyHV-3 infection through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune-suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3), as well as galectin 3 function by lncRNA, may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

Highlights

Cyprinid herpesvirus-3 (CyHV-3) infection is a major threat to common carp aquaculture [1], leading to widespread mortality and substantial economic loss
For group SvS-BvN-D7, “BS-advantage” represented the upregulated genes related to the breeding strain, while “NBS-advantage” represented the downregulated genes related to nonbreeding strain, after the comparison between survivors from breeding strain and survivors from the non-breeding strain
This study demonstrated that the anti-CyHV-3 immune mechanisms of a breeding strain of common carp

Summary

Introduction

Cyprinid herpesvirus-3 (CyHV-3) infection is a major threat to common carp aquaculture [1], leading to widespread mortality and substantial economic loss. Since latency and persistent carrying of CyHV-3 exist in carp [2,3,4], genetic backgrounds are crucial in developing an understanding of resistance against the virus. Experimental infections of carp from pure lines or crosses have indicated the existence of a genetic background of resistance by divergent survival rates [2]. A markedly higher expression of immune-related genes involved in pathogen recognition, complement activation, major histocompatibility complex class I (MHC I)-restricted antigen presentation, and the development of adaptive mucosal immunity was noted in the more resistant R3 line. The diallelic cross of four European carp lines, including Polish ‘K’ and ‘R6’, Hungarian ‘R7’ and French ‘F’ has been done to select the resistant fish, and found that MH class II B genes of carp can affect immunity against CyHV-3 infection [6]. Carp strains of Asian origin, Amur wild carp, were shown to be more resistant to CyHV-3 than strains originating from Europe, such as the Prerov scale carp or koi carp from a breed in the Czech Republic [7]

Methods

Results

Conclusion