Bai Yulin, Wang Mei, Zhao Ji, Bai Huaqiang, Zhang Xinyi, Wang Jiaying, Ke Qiaozhen, Qu Ang, Pu Fei, Zheng Weiqiang, Zhou Tao, Xu Peng
State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
BMC Genomics. 2022 Mar 15;23(1):206. doi: 10.1186/s12864-022-08431-w.
Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea. Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker.
In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of C. irritans, in this study, by comparing transcriptome data from different tissues of L. crocea, we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of L. crocea gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein-protein interaction (PPI) network analysis identified 3 hub genes including NFKBIA, TNFAIP3 and CEBPB, and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method.
In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of L. crocea post C. irritans and the molecular mechanism of pathogenesis for cryptocaryonosis.
Skin and gills are important sources of pro-inflammatory molecules, and their gene expression patterns are tissue-specific after C. irritans infection. 15 DEGs and 5 DE lncRNAs were identified as hub regulatory elements after C. irritans infection The HIF-1 signaling pathway and the complement and coagulation cascade pathway may be key tissue-specific regulatory pathways in gills and skin, respectively.
由刺激隐核虫引起的隐核虫病是大黄鱼（Larimichthys crocea）的主要疾病之一，每年给大黄鱼养殖业造成巨大经济损失。尽管已有一些关于隐核虫病发病机制的研究，但对大黄鱼不同免疫器官的先天防御机制了解甚少。
为了分析长链非编码RNA和刺激隐核虫感染期间免疫器官之间特异性表达的基因的作用，在本研究中，通过比较大黄鱼不同组织的转录组数据，我们在鳃和皮肤中鉴定出组织特异性转录本，包括在鳃中鉴定出507个差异表达的长链非编码RNA和1592个差异表达基因，以及在皮肤中鉴定出110个差异表达的长链非编码RNA和1160个差异表达基因。此外，我们构建了大黄鱼鳃和皮肤的转录组共表达图谱，包括7503个长链非编码RNA（lncRNA）和23172个蛋白质编码基因。基因本体论（GO）注释和京都基因与基因组百科全书（KEGG）通路分析表明，鳃中的差异表达基因和差异表达长链非编码RNA的靶基因在与免疫相关的几个通路中特异性富集，如HIF-1信号通路。皮肤中差异表达长链非编码RNA和差异表达基因的靶基因在补体和凝血级联通路中特异性富集。蛋白质-蛋白质相互作用（PPI）网络分析鉴定出3个枢纽基因，包括NFKBIA、TNFAIP3和CEBPB，以及5个重要的差异表达长链非编码RNA，包括MSTRG.24134.4、MSTRG.3038.5、MSTRG.27019.3、MSTRG.26559.1和MSTRG.10983.1。使用定量实时PCR方法验证了6个随机选择的差异表达免疫相关基因的表达模式。
简而言之，我们的研究有助于探索刺激隐核虫感染后大黄鱼不同组织中长链非编码RNA和蛋白质编码基因之间的潜在相互作用以及隐核虫病的发病分子机制。
皮肤和鳃是促炎分子的重要来源，刺激隐核虫感染后它们的基因表达模式具有组织特异性。刺激隐核虫感染后鉴定出15个差异表达基因和5个差异表达长链非编码RNA作为枢纽调控元件。HIF-1信号通路和补体及凝血级联通路可能分别是鳃和皮肤中的关键组织特异性调控通路。
