Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection

Abstract

Background 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. Results 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. Conclusions 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. Highlights 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.

Analysis of complement system and its related factors in Alzheimer’s disease

“…Among the 23 genes previous studies have shown their correlation with AD, we have: GFAP [ 41 , 42 ], PDGFRβ [ 43 – 45 ], NFKBIA [ 46 ], TNFRSF1B [ 47 ], NOTCH1 [ 48 ], BCL6 [ 49 ], CSF1R [ 50 ], LEP [ 51 ], DCLRE1C [ 52 ], KCNJ10 [ 53 ], MAP2K1 [ 54 ], VIP [ 55 ], SNCA [ 56 ], ENO2 [ 57 ], SST [ 58 ], UCHL1 [ 59 ], HPRT1 [ 60 ], STAT4 [ 61 ], CD14 [ 62 ], ITGB2 [ 63 ], SPP1 [ 64 ], STX1A [ 65 ], and SYP [ 66 ]. And these genes are involved in the regulation of molecules associated with the complement system, for instance, GFAP [ 67 ], PDGFRβ [ 68 ], NFKBIA [ 69 ], TNFRSF1B [ 70 ], NOTCH1 [ 71 ], BCL6 [ 72 ], CSF1R [ 73 ], LEP [ 74 ], DCLRE1C [ 75 ], KCNJ10 [ 76 ], MAP2K1 [ 77 ], VIP [ 78 ], SNCA [ 79 ], ENO2 [ 80 ], SST [ 81 ], UCHL1 [ 82 ], HPRT1 [ 83 ], STAT4 [ 84 ], CD14 [ 85 ], ITGB2 [ 86 ], SPP1 [ 87 ], STX1A [ 88 ], and SYP [ 89 ]. However, few studies have discussed their role in AD pathology by modulating the complement system, our study may be a new perspective for our future exploration of the relationship between AD and the complement system.…”

Disruption of mstn Gene by CRISPR/Cas9 in Large Yellow Croaker (Larimichthys crocea)

“…Through long-period cultivation and trials, the arti cial breeding of L. crocea was overcame (Zhao et al, 2021). But with the increasing consumption and product need, germplasm was urged to be improved under the threat of diseases bursting frequently (Bai et al, 2022). Genomic editing technology had been applied to kinds of farm animals including pig, sheep, bream and carp to produce superior traits, which showed great prospect for optimizing genotypes of L. crocea.…”

Correction: Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection

“…Following publication of the original article [ 1 ], it was reported that the authorship panel was missing an equal contribution designation for Yuilin Bai and Mei Wang. The original article [ 1 ] has been updated to include this.…”