A new framework for host-pathogen interaction research

• Published in: Frontiers in immunology Vol. 13; p. 1066733
• Main Authors: Yu, Hong, Li, Li, Huffman, Anthony, Beverley, John, Hur, Junguk, Merrell, Eric, Huang, Hsin-Hui, Wang, Yang, Liu, Yingtong, Ong, Edison, Cheng, Liang, Zeng, Tao, Zhang, Jingsong, Li, Pengpai, Liu, Zhiping, Wang, Zhigang, Zhang, Xiangyan, Ye, Xianwei, Handelman, Samuel K, Sexton, Jonathan, Eaton, Kathryn, Higgins, Gerry, Omenn, Gilbert S, Athey, Brian, Smith, Barry, Chen, Luonan, He, Yongqun
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 15.12.2022
• Subjects: bioinformatics; coronavirus infectious disease ontology (CIDO); COVID-19; disease outcome; host-coronavirus interaction; host-pathogen interaction; Host-Pathogen Interactions; Humans; Immunology; COVID-19; COVID-19 cocktail; host-pathogen interaction; host-coronavirus interaction; bioinformatics; disease outcome; coronavirus infectious disease ontology (CIDO); HPIPO framework
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2022.1066733

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed.