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Xiong N, Sun Q. Identifying COVID-19 subtypes by single-sample gene set enrichemnt analysis and providing guidance for sensitive drug selection. J Med Virol 2024; 96:e29497. [PMID: 38436142 DOI: 10.1002/jmv.29497] [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: 11/07/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
This study aimed at using single-sample gene set enrichment analysis scores to cluster naso/pharyngeal swab specimen samples from coronavirus disease 2019 (COVID-19) patients into two clusters. One cluster with higher fractions of immune cells and more active inflammatory-related pathways was called the Immunity-High (Immunity-H) group, and the other one was called the Immunity-Low group. We explored impacts of the method on COVID-19 treatment. First, given that the Immunity-H group was mainly enriched in inflammatory-related pathways and had higher fractions of inflammatory cells, the Immunity-H group may obtain more curative effects from anti-inflammatory treatment. Second, we searched some hot genes from the PubMed platform that had been studied by researchers and found these genes upregulated in the Immunity-H group, so we speculated the Immunity-H group and Immunity-Low group may have different curative effects from drugs targeting these genes. Finally, we screened out hub genes for the Immunity-H group and predicted potential drugs for these hub genes by a public data set (http://dgidb.genome.wustl.edu). These hub genes are significantly upregulated in the Immunity-H group and neutrophils so that the Immunity-H group may obtain different treatment results from potential drugs compared with the Immunity-Low group. Therefore, the cluster method may provide help in drug development and administration for COVID-19 patients.
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Affiliation(s)
- Nan Xiong
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
- Graduate School of Kunming Medical University, Kunming, China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
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Welén K, Rosendal E, Freyhult E, Oh WK, Gisslén M, Ahlm C, Connolly AMF, Överby AK, Josefsson A. Reply to Carlos G. Wambier and Gerard J. Nau’s Letter to the Editor re: Karin Welén, Ebba Rosendal, Magnus Gisslén, et al. A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2021.12.013. Positive Effects of Enzalutamide for Hospitalized COVID-19 Patients. Eur Urol 2022; 81:e143-e144. [PMID: 35248411 PMCID: PMC8864103 DOI: 10.1016/j.eururo.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Karin Welén
- Institute of Clinical Sciences, Department of Urology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ebba Rosendal
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Eva Freyhult
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - William K Oh
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magnus Gisslén
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Anne-Marie Fors Connolly
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden; The Laboratory for Molecular Infection Medicine Sweden, Umeå, Sweden
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden; The Laboratory for Molecular Infection Medicine Sweden, Umeå, Sweden
| | - Andreas Josefsson
- Institute of Clinical Sciences, Department of Urology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Surgical and Perioperative Sciences, Urology & Andrology, Umeå University, Umeå, Sweden; Wallenberg Center for Molecular Medicine, Umeå University, Umeå, Sweden.
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