Pathogenic Mechanism of a Highly Virulent Infectious Hematopoietic Necrosis Virus in Head Kidney of Rainbow Trout (Oncorhynchus mykiss) Analyzed by RNA-Seq Transcriptome Profiling

Abstract

Infectious hematopoietic necrosis virus (IHNV) is a pathogen that causes high rates of mortality in salmonid fishes. Therefore, an RNA-seq-based transcriptome analysis was performed in the head kidney of rainbow trout infected with a highly virulent IHNV strain to understand the pathogenesis of and defense strategies for IHNV infection in rainbow trout. The results showed that the numbers of DEGs were 618, 2626, and 774 (control vs. IHNV) on days 1, 3, and 5, respectively. Furthermore, the enrichment analysis of gene ontology (GO) annotations to classify DEGs showed that GO terms considerably associated with DEGs were gluconeogenesis, inflammatory response, and cell adhesion in the Biological Process (BP) category, apical plasma membrane, extracellular matrix (ECM) in the Cellular Component category, and transporter activity, integrin binding, and protein homodimerization activity in the Molecular Function category, on days 1, 3, and 5, respectively. Notably, GO terms in the BP category, including the negative regulation of type I interferon production and positive regulation of interleukin-1β secretion, were commonly identified at all time points. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, complement and coagulation cascades were commonly identified at all time points. Importantly, the widely recognized GO terms and KEGG pathways extensively linked to DEGs were related to energy metabolism on day 1, the immune response on day 3, and cell proliferation on day 5. Furthermore, protein–protein interaction networks and centrality analysis showed that the metabolism and signaling transduction pathways were majorly upregulated. Conclusively, the virulent IHNV infection drives pathogenesis by activating the metabolic energy pathway for energy use for viral replication, facilitating necrosis through autophagy, and causing a shutoff response of the host immune system through the downregulation of type I IFN at the initial stage of infection.

Transcriptome Profiling of Oncorhynchus mykiss Infected with Low or Highly Pathogenic Viral Hemorrhagic Septicemia Virus (VHSV)

“…Furthermore, TRIM63 is also probably involved in other processes (e.g., targeting pro-anabolic factors, intracellular trafficking) and, as other members of its family, seems to have emerging roles in innate immunity, since it is induced by IFNs [ 45 , 46 ]. Interestingly, Kim et al found TRIM25 , a protein belonging to the same family as the above mentioned one, among up-regulated DEGs in rainbow trout infected with a highly virulent strain of infectious hematopoietic necrosis virus (IHNV; family Rhabdoviridae ) [ 47 ].…”

“…Notably, some GO terms related to the immune system appeared identical in both strains in terms of timing and score, e.g., “tumour necrosis factor-mediated signalling pathway” and “regulation of interferon-gamma-mediated signalling pathway”. Regarding the latter GO, Kim et al [ 47 ] reported its enrichment at 3 dpi during a similar experimental trial performed using the other salmonid Novirhadbovirus (IHNV). Tumour necrosis factor (TNF) is a type II transmembrane protein expressed in the plasma [ 69 ].…”

TGF‐β1 Inhibits Osteoclast Differentiation and Abnormal Angiogenesis in Intervertebral Disc Degeneration: Evidence from RNA Sequencing and Animal Studies

“…The screening criteria for differentially expressed genes (DEGs) were |logFC| > 1 and FDR <0.05. Finally, mRNAs differentially expressed in IDD were obtained 27 …”

“…Finally, mRNAs differentially expressed in IDD were obtained. 27 Screening for Core Genes of IDD in the Mouse Model Differentially expressed mRNAs from mice with IDD were obtained based on the transcriptome sequencing difference analysis. the GeneCard database was used, and with "Intervertebral disc degeneration" as the search condition, the top 1000 genes were selected as the genes related to IDD by "Relevance score."…”

Dietary supplementation of Chinese herbal medicines enhances the immune response and resistance of rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus

“…Intensive farming conditions have contributed to economic growth while also leading to complex aquatic environments that make rainbow trout susceptible to pathogens ( 3 ). Infectious hematopoietic necrosis virus (IHNV), which belongs to the genus Novirhabdovirus of the family Rhabdoviridae, is highly pathogenic and widely transmissible, causing not only high mortality in rainbow trout but also brings huge economic losses to the global aquaculture industry ( 4 , 5 ). Vaccines have long been the main choice for preventing viral diseases, but their efficacy is limited by financial constraints.…”