# Transcriptome Analysis and Hub Gene Identification in the Brain Cell Lines of the Spotted Knifejaw (Oplegnathus punctatus) After Poly (I:C) Stimulation

## TL;DR

This study explores how brain cells in spotted knifejaw respond to a viral mimic, identifying key genes and pathways involved in immune responses.

## Contribution

The study identifies hub genes and immune pathways in brain cells of spotted knifejaw after poly (I:C) stimulation, offering new insights for disease-resistant breeding.

## Key findings

- 3169-3262 differentially expressed genes were identified at various time points after poly (I:C) stimulation.
- Immune-related pathways like NOD-like receptor and RIG-I-like receptor were significantly enriched.
- 30 hub genes were identified through protein–protein interaction network analysis.

## Abstract

The spotted knifejaw (Oplegnathus punctatus) has emerged as a species with substantial potential for aquaculture development in China. However, its industrial cultivation is severely constrained by viral diseases. Among these, viral nervous necrosis (VNN), caused by nervous necrosis virus (NNV), represents a critical bottleneck to the sustainable development of this industry. In order to elucidate the immune response mechanisms of the brain cells of spotted knifejaw, this study established a poly (I:C) stimulation model in vitro and performed transcriptomic sequencing to analyze the differentially expressed genes (DEGs) after stimulation. There were 3169, 3228, and 3262 DEGs at 3 h, 6 h, and 12 h compared to 0 h (control), respectively. Co-expression time clustering of DEGs identified two gene clusters (cluster 6 and cluster 10), which included several immune-related genes. GO and KEGG enrichment analyses indicated that DEGs among the four time points were significantly enriched in immune signaling pathways, including the NOD-like receptor, RIG-I-like receptor, C-type lectin receptor, and Toll-like receptor pathways, as well as disease-response pathways. In total, 1398 common DEGs were identified among three comparative groups, which delineated six interaction clusters and 30 hub genes in protein–protein interaction (PPI) network analysis. By integrating a cellular model with transcriptomics, this study provides preliminary insights into the molecular immune mechanisms underlying the response of brain cells to poly (I:C) stimulation, offering important theoretical support for future research on disease-resistant breeding and disease control strategies in spotted knifejaw.