Frontiers in Immunology (Dec 2022)
A new framework for host-pathogen interaction research
- Hong Yu,
- Hong Yu,
- Li Li,
- Anthony Huffman,
- John Beverley,
- John Beverley,
- Junguk Hur,
- Eric Merrell,
- Hsin-hui Huang,
- Hsin-hui Huang,
- Yang Wang,
- Yang Wang,
- Yang Wang,
- Yingtong Liu,
- Edison Ong,
- Liang Cheng,
- Tao Zeng,
- Jingsong Zhang,
- Pengpai Li,
- Zhiping Liu,
- Zhigang Wang,
- Xiangyan Zhang,
- Xiangyan Zhang,
- Xianwei Ye,
- Xianwei Ye,
- Samuel K. Handelman,
- Jonathan Sexton,
- Kathryn Eaton,
- Gerry Higgins,
- Gilbert S. Omenn,
- Brian Athey,
- Barry Smith,
- Luonan Chen,
- Yongqun He
Affiliations
- Hong Yu
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and National Health Commission (NHC) Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou Province, Guiyang, Guizhou, China
- Hong Yu
- Department of Basic Medicine, Guizhou University Medical College, Guiyang, Guizhou, China
- Li Li
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Anthony Huffman
- University of Michigan Medical School, Ann Arbor, MI, United States
- John Beverley
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States
- John Beverley
- Asymmetric Operations Sector, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
- Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
- Eric Merrell
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States
- Hsin-hui Huang
- University of Michigan Medical School, Ann Arbor, MI, United States
- Hsin-hui Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
- Yang Wang
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and National Health Commission (NHC) Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou Province, Guiyang, Guizhou, China
- Yang Wang
- Department of Basic Medicine, Guizhou University Medical College, Guiyang, Guizhou, China
- Yang Wang
- University of Michigan Medical School, Ann Arbor, MI, United States
- Yingtong Liu
- University of Michigan Medical School, Ann Arbor, MI, United States
- Edison Ong
- University of Michigan Medical School, Ann Arbor, MI, United States
- Liang Cheng
- Department of Bioinformatics, Harbin Medical University, Harbin, Helongjian, China
- Tao Zeng
- 0Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- Jingsong Zhang
- 0Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- Pengpai Li
- 1Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China
- Zhiping Liu
- 1Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China
- Zhigang Wang
- 2Department of Biomedical Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Xiangyan Zhang
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and National Health Commission (NHC) Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou Province, Guiyang, Guizhou, China
- Xiangyan Zhang
- Department of Basic Medicine, Guizhou University Medical College, Guiyang, Guizhou, China
- Xianwei Ye
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and National Health Commission (NHC) Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou Province, Guiyang, Guizhou, China
- Xianwei Ye
- Department of Basic Medicine, Guizhou University Medical College, Guiyang, Guizhou, China
- Samuel K. Handelman
- University of Michigan Medical School, Ann Arbor, MI, United States
- Jonathan Sexton
- University of Michigan Medical School, Ann Arbor, MI, United States
- Kathryn Eaton
- University of Michigan Medical School, Ann Arbor, MI, United States
- Gerry Higgins
- University of Michigan Medical School, Ann Arbor, MI, United States
- Gilbert S. Omenn
- University of Michigan Medical School, Ann Arbor, MI, United States
- Brian Athey
- University of Michigan Medical School, Ann Arbor, MI, United States
- Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States
- Luonan Chen
- 0Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- Yongqun He
- University of Michigan Medical School, Ann Arbor, MI, United States
- DOI
- https://doi.org/10.3389/fimmu.2022.1066733
- Journal volume & issue
-
Vol. 13
Abstract
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.
Keywords
- host-pathogen interaction
- disease outcome
- COVID-19
- host-coronavirus interaction
- coronavirus infectious disease ontology (CIDO)
- bioinformatics
