Elucidating the pathogenesis of enterovirus A71 infection using a multi-omics approach

Abstract

Enterovirus A71 (EV-A71) is an important human-pathogenic virus that causes epidemics of hand, foot, and mouth disease (HFMD) especially among children in the Asia-Pacific region. Severe EV-A71 infection may be associated with life-threatening neurological and cardiopulmonary complications. However, the pathogenesis underlying these severe complications remain incompletely understood and effective antiviral treatment for EV-A71 infection is currently lacking. To provide novel understanding on these knowledge gaps, lipidomics and metabolomics were applied in this thesis to characterize the changes in the host lipidome and metabolome upon EV-A71 infection.

In Chapter 2, ultra-high performance liquid chromatography–electrospray ionization–quadrupole–time of flight-mass spectrometry (UPLC-ESI-Q-TOF-MS)-based lipidomics was performed to characterize the host lipidome changes in rhabdomyosarcoma (RD) cells upon EV-A71 and the closely related coxsackievirus A16 (CV-A16) infections. The results revealed that 47 lipids within 11 lipid classes were significantly perturbed after these enterovirus infections. Four polyunsaturated fatty acids (PUFAs) including arachidonic acid (AA), docosahexaenoic acid (DHA), docosapentaenoic acid (DPA), and eicosapentaenoic acid (EPA) were identified to be consistently upregulated in enterovirus infection. Additionally, exogenously supplying of AA, DHA, or EPA in cell culture resulted in significantly decreased viral replication. Taken together, these results demonstrated that host lipids were specifically modulated for optimal virus replication during enterovirus infection and these lipids may be potential host-based antiviral targets.

In Chapter 3, a targeted quantitation of polar metabolites by gas-chromatography-tandem mass spectrometry (GC-MS/MS) was conducted. A total of 14 candidate metabolites with differentially expression profiles were identified in EV-A71-infected human induced pluripotent stem cells (iPSCs) derived neural progenitor cells (NPCs). The glycolysis pathway was identified to be playing a key role in EV-A71 infection according to pathway enrichment analysis. Importantly, the inhibition of one of the key enzymes of glycolysis, 6-phosphofructo-2-kinase (PFKFB3), was found to significantly suppress EV-A71 infection in vitro. The inhibitor of PFKFB3, KAN0438757, showed broad-spectrum antiviral activity against various enteroviruses, including EV-A71, CVB2 and PV-3. Collectively, these results demonstrated that manipulation of host metabolites profile might be a potential host-targeting antiviral strategy for enterovirus infection.

In summary, this thesis utilized a multi-omics approach to provide insights on EVA-71-induced changes on the host lipidome and metabolome. The significantly perturbed host lipids and metabolites identified in this thesis may have important roles in the pathogenesis and treatment strategy of EV-A71 and other enterovirus infections.