Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing

Abstract

The World Health Organisation reported in 2020 that six of the top 10 sources of death in low-income countries are parasites. Parasites are microorganisms in a relationship with a larger organism, the host. They acquire all benefits at the host’s expense. A disease develops if the parasitic infection disrupts normal functioning of the host. This disruption can range from mild to severe, including death. Humans and livestock continue to be challenged by established and emerging infectious disease threats. Vaccination is the most efficient tool for preventing current and future threats. Immunogenic proteins sourced from the disease-causing parasite are worthwhile vaccine components (subunits) due to reliable safety and manufacturing capacity. Publications with ‘subunit vaccine’ in their title have accumulated to thousands over the last three decades. However, there are possibly thousands more reporting immunogenicity results without mentioning ‘subunit’ and/or ‘vaccine’. The exact number is unclear given the non-standardised keywords in publications. The study aim is to identify parasite proteins that induce a protective response in an animal model as reported in the scientific literature within the last 30 years using machine learning and natural language processing. Source code to fulfil this aim and the vaccine candidate list obtained is made available.

Antigen discovery by bioinformatics analysis and peptide microarray for the diagnosis of cystic echinococcosis

“…Three software were used in parallel: TMHMM2 [ 17 ] was applied for the prediction of transmembrane helices, SignalP4 [ 18 ] to identify putative secreted proteins, and predGPI [ 19 ] to assess glycosylphosphatidylinositol (GPI)-anchored proteins. The immune system accessibility has been associated with the proteins exposed on the cell surfaces or secreted/excreted [ 20 ], all proteins that have been shown to be involved in host-immunity interactions [ 21 ]. Proteins that contain a signal peptide, as well as transmembrane proteins are accessible to the immune system and involved in several processes such as cell signaling and recognition [ 20 ].…”

“…The immune system accessibility has been associated with the proteins exposed on the cell surfaces or secreted/excreted [ 20 ], all proteins that have been shown to be involved in host-immunity interactions [ 21 ]. Proteins that contain a signal peptide, as well as transmembrane proteins are accessible to the immune system and involved in several processes such as cell signaling and recognition [ 20 ]. Moreover, the GPI-anchored proteins face the extracellular environment and have different functions including surface antigens, host-pathogen immune modulation and signaling, due to their localization on the external surface of the cells [ 19 ].…”