Leveraging lncRNA-miRNA-mRNA network to reveal anti-Spiroplasma eriocheiris infection mechanisms in Macrobrachium nipponense

Abstract

The oriental river prawn Macrobrachium nipponense (M. nipponense) is a commercially important shrimp susceptible to Spiroplasma eriocheiris (S. eriocheiris) infection. Long non-coding RNAs (lncRNAs) play critical roles in a host immune defense against invading pathogens through acting as competing endogenous RNAs (ceRNAs). However, the protective roles of lncRNAs associated ceRNAs in M. nipponense against S. eriocheiris infection remain largely unexplored. To address this problem, a comprehensive lncRNA-mRNA-miRNA network in the hemocyte of M. nipponense challenged with S. eriocheiris at different time points (0, 6, 24, and 48 h) was constructed in this study. The results showed that 238 differentially expressed lncRNAs (DElncRs), 3547 DEmRNAs, and 258 DEmiRNAs were identified during the challenge process. The target genes of DEmRNAs, DElncRNAs and DEmiRNAs were significantly enriched in multiple immune-related pathways, such as Toll-like receptor, PI3K-Akt, and TNF signaling pathways. The lncRNA associated ceRNAs network was also constructed, including 12 DElncRNAs, 23 DEmiRNAs, and 25 DETmRNAs. This network revealed that DElncRNAs (transcript_18441, transcript_11191, transcript_10673, transcript_10806, and transcript_17607), DEmiRNAs (miR-2c, miR-71-3p, miR-423-5p, and miR-423a), and DETmRNAs (ALF, PCE, and PPAE) were involved in M. nipponense immune defense against S. eriocheiris challenge. Taken together, our study identified crucial lncRNA associated ceRNA networks, playing pivotal roles in the immune response of M. nipponense against S. eriocheiris infection, and thus paving a novel avenue to develop strategies for spiroplasma disease prevention and control.