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Lu W, Ren H. Diseases spectrum in the field of spatiotemporal patterns mining of infectious diseases epidemics: A bibliometric and content analysis. Front Public Health 2023; 10:1089418. [PMID: 36699887 PMCID: PMC9868952 DOI: 10.3389/fpubh.2022.1089418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Numerous investigations of the spatiotemporal patterns of infectious disease epidemics, their potential influences, and their driving mechanisms have greatly contributed to effective interventions in the recent years of increasing pandemic situations. However, systematic reviews of the spatiotemporal patterns of communicable diseases are rare. Using bibliometric analysis, combined with content analysis, this study aimed to summarize the number of publications and trends, the spectrum of infectious diseases, major research directions and data-methodological-theoretical characteristics, and academic communities in this field. Based on 851 relevant publications from the Web of Science core database, from January 1991 to September 2021, the study found that the increasing number of publications and the changes in the disease spectrum have been accompanied by serious outbreaks and pandemics over the past 30 years. Owing to the current pandemic of new, infectious diseases (e.g., COVID-19) and the ravages of old infectious diseases (e.g., dengue and influenza), illustrated by the disease spectrum, the number of publications in this field would continue to rise. Three logically rigorous research directions-the detection of spatiotemporal patterns, identification of potential influencing factors, and risk prediction and simulation-support the research paradigm framework in this field. The role of human mobility in the transmission of insect-borne infectious diseases (e.g., dengue) and scale effects must be extensively studied in the future. Developed countries, such as the USA and England, have stronger leadership in the field. Therefore, much more effort must be made by developing countries, such as China, to improve their contribution and role in international academic collaborations.
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Affiliation(s)
- Weili Lu
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Ren
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China,*Correspondence: Hongyan Ren ✉
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Wang Z, Guo K, Gao P, Pu Q, Li C, Hur J, Wu M. Repurposable drugs for SARS-CoV-2 and influenza sepsis with scRNA-seq data targeting post-transcription modifications. PRECISION CLINICAL MEDICINE 2021; 4:215-230. [PMID: 34993416 PMCID: PMC8694063 DOI: 10.1093/pcmedi/pbab022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has impacted almost every part of human life worldwide, posing a massive threat to human health. The lack of time for new drug discovery and the urgent need for rapid disease control to reduce mortality have led to a search for quick and effective alternatives to novel therapeutics, for example drug repurposing. To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA-approved drugs and preclinical small-molecule compounds by integrating gene expression perturbation data for chemicals from the Library of Integrated Network-Based Cellular Signatures project with a publicly available single-cell RNA sequencing dataset from patients with mild and severe COVID-19 (GEO: GSE145926, public data available and accessed on 22 April 2020). We identified 281 FDA-approved drugs that have the potential to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 16 of which are currently undergoing clinical trials to evaluate their efficacy against COVID-19. We experimentally tested and demonstrated the inhibitory effects of tyrphostin-AG-1478 and brefeldin-a, two chemical inhibitors of glycosylation (a post-translational modification) on the replication of the single-stranded ribonucleic acid (ssRNA) virus influenza A virus as well as on the transcription and translation of host cell cytokines and their regulators (IFNs and ISGs). In conclusion, we have identified and experimentally validated repurposable anti-SARS-CoV-2 and IAV drugs using a systems biology approach, which may have the potential for treating these viral infections and their complications (sepsis).
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Affiliation(s)
- Zhihan Wang
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pan Gao
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
- Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Qinqin Pu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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Liu Y, Hur J, Chan WKB, Wang Z, Xie J, Sun D, Handelman S, Sexton J, Yu H, He Y. Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. Sci Data 2021; 8:16. [PMID: 33441564 PMCID: PMC7806933 DOI: 10.1038/s41597-021-00799-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
Our systematic literature collection and annotation identified 106 chemical drugs and 31 antibodies effective against the infection of at least one human coronavirus (including SARS-CoV, SAR-CoV-2, and MERS-CoV) in vitro or in vivo in an experimental or clinical setting. A total of 163 drug protein targets were identified, and 125 biological processes involving the drug targets were significantly enriched based on a Gene Ontology (GO) enrichment analysis. The Coronavirus Infectious Disease Ontology (CIDO) was used as an ontological platform to represent the anti-coronaviral drugs, chemical compounds, drug targets, biological processes, viruses, and the relations among these entities. In addition to new term generation, CIDO also adopted various terms from existing ontologies and developed new relations and axioms to semantically represent our annotated knowledge. The CIDO knowledgebase was systematically analyzed for scientific insights. To support rational drug design, a "Host-coronavirus interaction (HCI) checkpoint cocktail" strategy was proposed to interrupt the important checkpoints in the dynamic HCI network, and ontologies would greatly support the design process with interoperable knowledge representation and reasoning.
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Affiliation(s)
- Yingtong Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Junguk Hur
- University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Wallace K B Chan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Zhigang Wang
- Department of Biomedical Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Jiangan Xie
- School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samuel Handelman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- U-M Center for Drug Repurposing, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jonathan Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- U-M Center for Drug Repurposing, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hong Yu
- Department of Respiratory and Critical Care Medicine, Guizhou Province People's Hospital and NHC Key Laboratory of Immunological Diseases, People's Hospital of Guizhou University, Guiyang, Guizhou, 550002, China
- Department of Basic Medicine, Guizhou University Medical College, Guiyang, Guizhou, 550025, China
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Larson C, Oronsky B, Goyal S, Ray C, Hedjran F, Hammond TC, Kesari S, Caroen S, Lybeck M, Dobalian VE, Oronsky A, Reid T. COVID-19 and cancer: A guide with suggested COVID-19 rule-out criteria to support clinical decision-making. Biochim Biophys Acta Rev Cancer 2020; 1874:188412. [PMID: 32827582 PMCID: PMC7438345 DOI: 10.1016/j.bbcan.2020.188412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/21/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious zoonotic pathogen that has exacted heavy public health, social and economic tolls. In February 2020, the World Health Organization acronymed the disease caused by SARS-CoV-2 as COVID-19, for coronavirus disease 2019. The number of confirmed COVID-19 infections, which has been detected in at least 103 countries, has reached 1,970,225 worldwide as of April 14, 2020 with 124,544 deaths, according to the U.S. Centers for Disease Control and Prevention (CDC). Many cases of COVID-19 resolve quickly. However, the disease, which, like other respiratory pathogens that cause common cold symptoms is believed to be transmitted through respiratory droplets. Infection with COVID-19 can also lead to significant morbidity and death; this is particularly the case for cancer patients. Moreover, because the signs and symptoms of COVID-19 are easily misattributed to the sequelae of cancer itself, such as pulmonary embolism, or its treatment, such as nausea and diarrhea, diagnosis may be delayed or missed. Potential COVID-19 rule out criteria, based on the Wells' criteria for pulmonary embolism, another protean disease entity, are provided as a decision-making aid. This review summarizes the current understanding of the transmission, clinical presentation, diagnosis and differential diagnosis, pathogenesis, rationale to treat the cancer or not, treatment and prevention of COVID-19 with an emphasis on implications in cancer.
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Affiliation(s)
| | | | - Sharad Goyal
- George Washington University, Washington, DC, USA
| | - Carolyn Ray
- St. Francis Hospital and Medical Center, Hartford, CT, USA
| | | | - Terese C. Hammond
- John Wayne Cancer Institute at Providence St. John's Health, Santa Monica, CA, USA
| | - Santosh Kesari
- John Wayne Cancer Institute at Providence St. John's Health, Santa Monica, CA, USA
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5
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He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang HH, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Sci Data 2020; 7:181. [PMID: 32533075 PMCID: PMC7293349 DOI: 10.1038/s41597-020-0523-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 11/15/2022] Open
Abstract
The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
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Affiliation(s)
- Yongqun He
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Hong Yu
- People's Hospital of Guizhou Province, Guiyang, Guizhou, 550002, China
- Guizhou University Medical College, Guiyang, Guizhou, 550025, China
| | - Edison Ong
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yang Wang
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- People's Hospital of Guizhou Province, Guiyang, Guizhou, 550002, China
- Guizhou University Medical College, Guiyang, Guizhou, 550025, China
| | - Yingtong Liu
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anthony Huffman
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Hsin-Hui Huang
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- National Yang-Ming University, Taipei, 112-21, Taiwan
| | | | - Junguk Hur
- University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA
| | - Xiaolin Yang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Gilbert S Omenn
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brian Athey
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Barry Smith
- University at Buffalo, Buffalo, NY, 14260, USA
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6
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Wang Z, Guo K, Gao P, Pu Q, Wu M, Li C, Hur J. Identification of Repurposable Drugs and Adverse Drug Reactions for Various Courses of COVID-19 Based on Single-Cell RNA Sequencing Data. ARXIV 2020:arXiv:2005.07856v2. [PMID: 33299905 PMCID: PMC7724679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 12/04/2020] [Indexed: 10/26/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has impacted almost every part of human life worldwide, posing a massive threat to human health. There is no specific drug for COVID-19, highlighting the urgent need for the development of effective therapeutics. To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA-approved drugs and preclinical small-molecule compounds by integrating the gene expression perturbation data for chemicals from the Library of Integrated Network-Based Cellular Signatures project with a publicly available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We identified 281 FDA-approved drugs that have the potential to be effective against SARS-CoV-2 infection, 16 of which are currently undergoing clinical trials to evaluate their efficacy against COVID-19. We experimentally tested the inhibitory effects of tyrphostin-AG-1478 and brefeldin-a on the replication of the single-stranded ribonucleic acid (ssRNA) virus influenza A virus. In conclusion, we have identified a list of repurposable anti-SARS-CoV-2 drugs using a systems biology approach.
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Affiliation(s)
- Zhihan Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Kai Guo
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Pan Gao
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Qinqin Pu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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