Integrated transcriptomic and metabolomic analysis reveals ApoLp-III-mediated BmNPV suppression via host energy and lipid reprogramming

In global sericulture, the most economically important and primary causative pathogen is Bombyx mori nucleopolyhedrovirus (BmNPV), but the host immune metabolism that restricts the viral replication is not completely defined. A recently identified insect multifunctional apolipoprotein (apolipophorin-III [ApoLp-III]) was shown to suppress BmNPV proliferation by enhancing ceramide accumulation. However, it is unknown how this antiviral action is mediated through coordinated transcriptional and metabolic changes. In this study, we dissect the ApoLp-III-mediated antiviral mechanism by constructing an ApoLp-III-overexpressing BmN cell line and integrating RNA-seq data with a previously published metabolomic profile. A total of 1067 differentially expressed genes (DEGs) with significantly opposing expression trends were identified. These DEGs were prominent in DNA replication, oxidative phosphorylation (OXPHOS) and amino sugar nucleotide sugar metabolism. Genes associated with amino acid metabolism were down-regulated, while genes linked with DNA replication and OXPHOS were up-regulated. Bidirectional regulation of sphingolipids was also confirmed by quantitative real-time PCR (qRT-PCR) and transcriptomic data. Ceramide accumulation resulted from the down-regulation of alkaline ceramidase (ACER) and up-regulation of regulatory subunit of the rate-limiting ceramide synthesis enzyme, SPTssA. Integrated multi-omics correlation analysis further showed that ceramide species positively correlated with OXPHOS and negatively correlated with amino sugar metabolism. Meanwhile, down-regulated triglycerides showed negative correlation with DNA replication and OXPHOS genes. In addition, we identified ApoLp-III interacting proteins, that is, the integrin-associated cytoskeletal regulator, Talin-1 and lepidopteran-specific immune receptor Haemolin, using Flag-based co-immunoprecipitation coupled with mass spectrometry. Our results show that ApoLp-III suppresses BmNPV replication by the coordinated reprogramming of host cellular energy (OXPHOS) and lipid (sphingolipid) metabolism. Thus, ApoLp-III acts as an important immunometabolic hub in the antiviral defence of lepidopterans, and our research also offers a theoretical foundation for controlling silkworm diseases by targeting sphingolipid-energy pathway.