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Zhang Z, Wang S, Jiang L, Wei J, Lu C, Li S, Diao Y, Fang Z, He S, Tan T, Yang Y, Zou K, Shi J, Lin J, Chen L, Bao C, Fei J, Fang H. Priority index for critical Covid-19 identifies clinically actionable targets and drugs. Commun Biol 2024; 7:189. [PMID: 38366110 PMCID: PMC10873402 DOI: 10.1038/s42003-024-05897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
While genome-wide studies have identified genomic loci in hosts associated with life-threatening Covid-19 (critical Covid-19), the challenge of resolving these loci hinders further identification of clinically actionable targets and drugs. Building upon our previous success, we here present a priority index solution designed to address this challenge, generating the target and drug resource that consists of two indexes: the target index and the drug index. The primary purpose of the target index is to identify clinically actionable targets by prioritising genes associated with Covid-19. We illustrate the validity of the target index by demonstrating its ability to identify pre-existing Covid-19 phase-III drug targets, with the majority of these targets being found at the leading prioritisation (leading targets). These leading targets have their evolutionary origins in Amniota ('four-leg vertebrates') and are predominantly involved in cytokine-cytokine receptor interactions and JAK-STAT signaling. The drug index highlights opportunities for repurposing clinically approved JAK-STAT inhibitors, either individually or in combination. This proposed strategic focus on the JAK-STAT pathway is supported by the active pursuit of therapeutic agents targeting this pathway in ongoing phase-II/III clinical trials for Covid-19.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lulu Jiang
- Translational Health Sciences, University of Bristol, Bristol, BS1 3NY, UK
| | - Jianwen Wei
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, W12 0HS, UK
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Yizhu Diao
- College of Finance and Statistics, Hunan University, Changsha, 410079, Hunan, China
| | - Zhongcheng Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuo He
- College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tingting Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yisheng Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kexin Zou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - James Lin
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| | - Jian Fei
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Brignoli T, Ferrara S, Bertoni G. Emerging In Vitro Models for the Study of Infection and Pathogenesis of Pseudomonas aeruginosa and Testing of Antibacterial Agents. Methods Mol Biol 2024; 2721:233-239. [PMID: 37819526 DOI: 10.1007/978-1-0716-3473-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Several animal models have been developed to study infection strategies and pathogenesis of Pseudomonas aeruginosa. Some of these models are also used in preclinical and clinical research. However, these models are increasingly showing their limitations, including in recapitulating human diseases such as cystic fibrosis, which is strongly linked to P. aeruginosa infection. The emerging field of human organoids and organs-on-a-chip is expected to provide answers to the need for in vitro modeling of human diseases. Here, we describe the first recent efforts that will hopefully provide the basis for the development of advanced in vitro models for the study of P. aeruginosa infection and pathogenesis and the testing of antibacterial agents.
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Affiliation(s)
- Tarcisio Brignoli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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Maia R, Carvalho V, Faria B, Miranda I, Catarino S, Teixeira S, Lima R, Minas G, Ribeiro J. Diagnosis Methods for COVID-19: A Systematic Review. MICROMACHINES 2022; 13:1349. [PMID: 36014271 PMCID: PMC9415914 DOI: 10.3390/mi13081349] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 05/15/2023]
Abstract
At the end of 2019, the coronavirus appeared and spread extremely rapidly, causing millions of infections and deaths worldwide, and becoming a global pandemic. For this reason, it became urgent and essential to find adequate tests for an accurate and fast diagnosis of this disease. In the present study, a systematic review was performed in order to provide an overview of the COVID-19 diagnosis methods and tests already available, as well as their evolution in recent months. For this purpose, the Science Direct, PubMed, and Scopus databases were used to collect the data and three authors independently screened the references, extracted the main information, and assessed the quality of the included studies. After the analysis of the collected data, 34 studies reporting new methods to diagnose COVID-19 were selected. Although RT-PCR is the gold-standard method for COVID-19 diagnosis, it cannot fulfill all the requirements of this pandemic, being limited by the need for highly specialized equipment and personnel to perform the assays, as well as the long time to get the test results. To fulfill the limitations of this method, other alternatives, including biological and imaging analysis methods, also became commonly reported. The comparison of the different diagnosis tests allowed to understand the importance and potential of combining different techniques, not only to improve diagnosis but also for a further understanding of the virus, the disease, and their implications in humans.
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Affiliation(s)
- Renata Maia
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Violeta Carvalho
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
- MEtRICs, Mechanical Engineering Department, Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- ALGORITMI, Production and Systems Department, School of Engineering, Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
| | - Bernardo Faria
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Inês Miranda
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Susana Catarino
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Senhorinha Teixeira
- ALGORITMI, Production and Systems Department, School of Engineering, Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
| | - Rui Lima
- MEtRICs, Mechanical Engineering Department, Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- CEFT, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
- ALiCE, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Graça Minas
- Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, Campus de Azurém, University of Minho, Guimarães, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João Ribeiro
- ALiCE, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
- Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal
- Centro de Investigação de Montanha (CIMO), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal
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