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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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Marocco R, Carraro A, Zingaropoli MA, Nijhawan P, Tortellini E, Guardiani M, Mengoni F, Zuccalà P, Belvisi V, Kertusha B, Parente A, Del Borgo C, Vullo V, Ciardi M, Mastroianni CM, Lichtner M. Role of Tocilizumab in Down Regulating sCD163 Plasmatic Levels in a Cohort of COVID-19 Patients. Front Immunol 2022; 13:871592. [PMID: 35444637 PMCID: PMC9013773 DOI: 10.3389/fimmu.2022.871592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background CD163, a haptoglobin-hemoglobin scavenger receptor mostly expressed by monocytes and macrophages, is involved in the regulation of inflammatory processes. Following proteolytic cleavage after pro-inflammatory stimulation, CD163 is shed from the cell surface and its soluble form in plasma, sCD163, is a biomarker of monocyte/macrophage lineage activation. The assessment of sCD163 plasmatic levels in an early stage of the disease could have clinical utility in predicting the severity of COVID-19 pneumonia. The use of tocilizumab (monoclonal antibody anti-IL-6 receptor) in COVID-19 patients reduces lethality rate at 30 days. The aim of the study was to investigate the effect of tocilizumab on sCD163 plasmatic levels in a cohort of COVID-19 patients. Methods In COVID-19 patients, on hospital admission (T0), after 7 days from hospitalization (T7) and after 45 days from discharge (T45) sCD163 plasmatic levels were evaluated, along with other laboratory parameters. COVID-19 patients were stratified into tocilizumab (TCZ) and non-tocilizumab (non-TCZ) groups. TCZ group was further divided into responder (R) and non-responder (NR) groups. Patients who died or required mechanical ventilation were defined as NR. As control group, healthy donors (HD) were enrolled. Results Seventy COVID-19 patients and 47 HD were enrolled. At T0, sCD163 plasmatic levels were higher in COVID-19 patients compared to HD (p<0.0001) and the longitudinal evaluation showed a reduction in sCD163 plasmatic levels at T7 compared to T0 (p=0.0211). At T0, both TCZ and non-TCZ groups showed higher sCD163 plasmatic levels compared to HD (p<0.0001 and p=0.0147, respectively). At T7, the longitudinal evaluation showed a significant reduction in sCD163 plasmatic levels (p=0.0030) only in the TCZ group, reaching levels comparable to those of HD. Conversely, not statistically significance in non-TCZ group was observed and, at T7, a statistically significance was found comparing non-TCZ group to HD (p=0.0019). At T0, R and NR groups showed not statistically significance in sCD163 plasmatic levels and both groups showed higher levels compared to HD (p=0.0001 and p=0.0340, respectively). The longitudinal evaluation showed significant reductions in both groups (R: p=0.0356; NR: p=0.0273) independently of the outcome. After 45 days of follow-up sCD163 plasmatic levels remain stable. Conclusion sCD163 plasmatic levels are increased in COVID-19 pneumonia and is efficiently down-regulated by tocilizumab treatment regardless of the clinical outcome.
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Affiliation(s)
- Raffaella Marocco
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
| | - Anna Carraro
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Antonella Zingaropoli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- *Correspondence: Maria Antonella Zingaropoli,
| | - Parni Nijhawan
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Eeva Tortellini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mariasilvia Guardiani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Fabio Mengoni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paola Zuccalà
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
| | - Valeria Belvisi
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
| | - Blerta Kertusha
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alberico Parente
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Cosmo Del Borgo
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
| | - Vincenzo Vullo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Rosa Ciardi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Miriam Lichtner
- Infectious Diseases Unit, Santa Maria (SM) Goretti Hospital, Sapienza University of Rome, Latina, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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Barbara I, Silvia M, Dario T, Giuseppe C, Stallone G. Case Report: Tocilizumab for Acute Kidney Graft Dysfunction in Patient Affected by COVID-19. Front Med (Lausanne) 2021; 8:732792. [PMID: 34901054 PMCID: PMC8655874 DOI: 10.3389/fmed.2021.732792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was isolated in January 2020 and, on March, the WHO declared the status of a pandemic. It causes a cytokine release syndrome, called “cytokine storm,” characterized by systemic inflammation involving elevated levels of cytokines and hyperactivation of immune cell; this profound alteration in the immune system led to an overshooting inflammatory response contributing to morbidity and mortality. Solid organ transplant recipients are at particularly higher risk of developing critical coronavirus disease 2019 (COVID-19) due to chronic immunosuppression; in fact, establishing the balance between infection and rejection in any transplant recipient is the principal aim when prescribing immunosuppression. Tocilizumab, a humanized monoclonal antibody against interleukin-6 (IL-6) receptor widely adopted in adult rheumatoid arthritis, is used as rescue therapy for chronic antibody-mediated rejection in kidney transplantation. Data about the use of tocilizumab for treating acute kidney graft dysfunction in a setting of kidney-transplanted patients affected by COVID-19 are lacking. In this case study, we discuss the case of kidney transplant recipient with proven SARS-CoV-2 infection that develops acute graft dysfunction and the management of immunosuppression with concomitant tocilizumab administration.
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Affiliation(s)
- Infante Barbara
- Nephrology Dialysis and Transplantation Unit, University of Foggia, Foggia, Italy
| | - Mercuri Silvia
- Nephrology Dialysis and Transplantation Unit, University of Foggia, Foggia, Italy
| | - Troise Dario
- Nephrology Dialysis and Transplantation Unit, University of Foggia, Foggia, Italy
| | - Castellano Giuseppe
- Nephrology Dialysis and Transplantation Unit, University of Foggia, Foggia, Italy.,Unit of Nephrology, Dialysis and Renal Transplantation-Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca'Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Giovanni Stallone
- Nephrology Dialysis and Transplantation Unit, University of Foggia, Foggia, Italy
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