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Wang J, Liu J, Luo M, Cui H, Zhang W, Zhao K, Dai H, Song F, Chen K, Yu Y, Zhou D, Li MJ, Yang H. Rational drug repositioning for coronavirus-associated diseases using directional mapping and side-effect inference. iScience 2022; 25:105348. [PMID: 36267550 PMCID: PMC9556799 DOI: 10.1016/j.isci.2022.105348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen of coronavirus disease 2019 (COVID-19), has infected hundreds of millions of people and caused millions of deaths. Looking for valid druggable targets with minimal side effects for the treatment of COVID-19 remains critical. After discovering host genes from multiscale omics data, we developed an end-to-end network method to investigate drug-host gene(s)-coronavirus (CoV) paths and the mechanism of action between the drug and the host factor in a directional network. We also inspected the potential side effect of the candidate drug on several common comorbidities. We established a catalog of host genes associated with three CoVs. Rule-based prioritization yielded 29 Food and Drug Administration (FDA)-approved drugs via accounting for the effects of drugs on CoVs, comorbidities, and drug-target confidence information. Seven drugs are currently undergoing clinical trials as COVID-19 treatment. This catalog of druggable host genes associated with CoVs and the prioritized repurposed drugs will provide a new sight in therapeutics discovery for severe COVID-19 patients.
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Affiliation(s)
- Jianhua Wang
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China,Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiaojiao Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Menghan Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hui Cui
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenwen Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dongming Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China,Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
| | - Hongxi Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
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Dopazo J, Maya-Miles D, García F, Lorusso N, Calleja MÁ, Pareja MJ, López-Miranda J, Rodríguez-Baño J, Padillo J, Túnez I, Romero-Gómez M. Implementing Personalized Medicine in COVID-19 in Andalusia: An Opportunity to Transform the Healthcare System. J Pers Med 2021; 11:475. [PMID: 34073493 PMCID: PMC8226500 DOI: 10.3390/jpm11060475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic represents an unprecedented opportunity to exploit the advantages of personalized medicine for the prevention, diagnosis, treatment, surveillance and management of a new challenge in public health. COVID-19 infection is highly variable, ranging from asymptomatic infections to severe, life-threatening manifestations. Personalized medicine can play a key role in elucidating individual susceptibility to the infection as well as inter-individual variability in clinical course, prognosis and response to treatment. Integrating personalized medicine into clinical practice can also transform health care by enabling the design of preventive and therapeutic strategies tailored to individual profiles, improving the detection of outbreaks or defining transmission patterns at an increasingly local level. SARS-CoV2 genome sequencing, together with the assessment of specific patient genetic variants, will support clinical decision-makers and ultimately better ways to fight this disease. Additionally, it would facilitate a better stratification and selection of patients for clinical trials, thus increasing the likelihood of obtaining positive results. Lastly, defining a national strategy to implement in clinical practice all available tools of personalized medicine in COVID-19 could be challenging but linked to a positive transformation of the health care system. In this review, we provide an update of the achievements, promises, and challenges of personalized medicine in the fight against COVID-19 from susceptibility to natural history and response to therapy, as well as from surveillance to control measures and vaccination. We also discuss strategies to facilitate the adoption of this new paradigm for medical and public health measures during and after the pandemic in health care systems.
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Affiliation(s)
- Joaquín Dopazo
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Área de Bioinformática, Fundación progreso y Salud, Junta de Andalucía, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Douglas Maya-Miles
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
| | - Federico García
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria IBS, 18012 Granada, Spain
| | - Nicola Lorusso
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Dirección General de Salud Pública, Consejería de Salud y Familias, Junta de Andalucía, Spain
| | - Miguel Ángel Calleja
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Farmacia, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | - María Jesús Pareja
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Hospital Universitario de Valme, 41014 Sevilla, Spain
| | - José López-Miranda
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Medicina Interna, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Córdoba, Spain
- Departamento de Ciencias Médicas y Quirúrgicas, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Jesús Rodríguez-Baño
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
| | - Javier Padillo
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Departamento de Cirugía, Universidad de Sevilla, 41009 Sevilla, Spain
- Servicio de Cirugía General y Digestiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Isaac Túnez
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Servicio de Medicina Interna, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Córdoba, Spain
- Departamento de Bioquímica, Universidad de Córdoba, 14071 Córdoba, Spain
- Secretaría General de Investigación, Desarrollo e Innovación en Salud, Consejería de Salud y Familias de la Junta de Andalucía, 41020 Sevilla, Spain
| | - Manuel Romero-Gómez
- GT MP Covid-19. SGIDIS, Consejería de Salud y Familias, Junta de Andalucía, Spain; (J.D.); (F.G.); (N.L.); (M.Á.C.); (M.J.P.); (J.L.-M.); (J.R.-B.); (J.P.)
- Instituto de Biomedicina de Sevilla (HUVR/HUVM/CSIC/US), 41013 Sevilla, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Servicio de Aparato Digestivo, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
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D’Antonio M, Arthur TD, Nguyen JP, Matsui H, D’Antonio-Chronowska A, Frazer KA. Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.10.21256423. [PMID: 34013287 PMCID: PMC8132261 DOI: 10.1101/2021.05.10.21256423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we applied colocalization to compare summary statistics for 16 GWASs from the COVID-19 Host Genetics Initiative to investigate similarities and differences in their genetic signals. We identified 9 loci associated with susceptibility (one with two independent GWAS signals; one with an ethnicity-specific signal), 14 associated with severity (one with two independent GWAS signals; two with ethnicity-specific signals) and one harboring two discrepant GWAS signals (one for susceptibility; one for severity). Utilizing colocalization we also identified 45 GTEx tissues that had eQTL(s) for 18 genes strongly associated with GWAS signals in eleven loci (1-4 genes per locus). Some of these genes showed tissue-specific altered expression and others showed altered expression in up to 41 different tissue types. Our study provides insights into the complex molecular mechanisms underlying inherited predispositions to COVID-19-disease phenotypes.
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Affiliation(s)
- Matteo D’Antonio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Timothy D. Arthur
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer P. Nguyen
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A. Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
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