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Sokouti B. A systems biology approach for investigating significantly expressed genes among COVID-19, hepatocellular carcinoma, and chronic hepatitis B. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:146. [PMID: 37521843 PMCID: PMC9584277 DOI: 10.1186/s43042-022-00360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 01/08/2023] Open
Abstract
Background Worldwide, COVID-19's death rate is about 2%, considering the incidence and mortality. However, the information on its complications in other organs, specifically the liver and its disorders, is limited in mild or severe cases. In this study, we aimed to computationally investigate the typical relationships between liver-related diseases [i.e., hepatocellular carcinoma (HCC), and chronic hepatitis B (CHB)] and COVID-19, considering the involved significant genes and their molecular mechanisms. Methods We investigated two GEO microarray datasets (GSE164805 and GSE58208) to identify differentially expressed genes (DEGs) among the generated four datasets for mild/severe COVID-19, HCC, and CHB. Then, the overlapping genes among them were identified for GO and KEGG enrichment analyses, protein-protein interaction network construction, hub genes determination, and their associations with immune cell infiltration. Results A total of 22 significant genes (i.e., ACTB, ATM, CDC42, DHX15, EPRS, GAPDH, HIF1A, HNRNPA1, HRAS, HSP90AB1, HSPA8, IL1B, JUN, POLR2B, PTPRC, RPS27A, SFRS1, SMARCA4, SRC, TNF, UBE2I, and VEGFA) were found to play essential roles among mild/severe COVID-19 associated with HCC and CHB. Moreover, the analysis of immune cell infiltration revealed that these genes are mostly positively correlated with tumor immune and inflammatory responses. Conclusions In summary, the current study demonstrated that 22 identified DEGs might play an essential role in understanding the associations between the mild/severe COVID-19 patients with HCC and CHB. So, the HCC and CHB patients involved in different types of COVID-19 can benefit from immune-based targets for therapeutic interventions. Supplementary Information The online version contains supplementary material available at 10.1186/s43042-022-00360-3.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Kerachian MA, Amel Jamehdar S, Azghandi M, Keyvanlou N, Mozaffari-Jovin S, Javadmanesh A, Amini M. Developing novel liquid biopsy by selective capture of viral RNA on magnetic beads to detect COVID-19. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2022; 25:762-766. [PMID: 35949306 PMCID: PMC9320198 DOI: 10.22038/ijbms.2022.65260.14379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 11/07/2022]
Abstract
Objectives Early, specific, and sensitive detection methods of COVID-19 are essential for force stopping its worldwide infection. Although CT images of the lung and/or viral RNA extraction followed by real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) are widely used; they have some limitations. Here, we developed a highly sensitive magnetic bead-based viral RNA extraction assay followed by rRT-PCR. Materials and Methods Case group included oropharyngeal/nasopharyngeal and blood samples from 30 patients diagnosed positive by PCR test for COVID-19 and control group included 30 same samples from COVID-19 negative PCR test individuals. RNA was extracted, using viral RNA extraction kit as well as using our hand-made capture bead-based technique. A one-step cDNA synthesis and Real Time PCR was conducted. A two-step comparison of the different viral RNA extraction methods for oropharyngeal/nasopharyngeal and blood samples was performed. Student t-test was applied with a P<0.05 considered statistically significant. Results In the case group, all 30 mucosal samples extracted either with viral RNA extraction kit or with beads-based assay were COVID-19 positive although in the latter category, Cqs were much lower. Although 43% of plasma samples extracted by bead-based method were found to be positive but no plasma samples extracted with column-based kit were detected positive by Real Time PCR. Conclusion Bead-based RNA extraction method can reduce RNA loss by its single-tube performance and enhance the test sensitivity. It is also more sensitive to lower viral loads as shown in the detection of blood samples and the lower Cqs of mucosal samples.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran,Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran,Corresponding author: Mohammad Amin Kerachian. Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. Tel/ Fax: +98-5138002244;
| | - Saeid Amel Jamehdar
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marjan Azghandi
- Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran,Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Nasrin Keyvanlou
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran,Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahnaz Amini
- Lung Diseases Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Spagnolello O, Pinacchio C, Santinelli L, Vassalini P, Innocenti GP, De Girolamo G, Fabris S, Giovanetti M, Angeletti S, Russo A, Mastroianni CM, Ciccozzi M, Ceccarelli G, d'Ettorre G. Targeting Microbiome: An Alternative Strategy for Fighting SARS-CoV-2 Infection. Chemotherapy 2021; 66:24-32. [PMID: 33756475 PMCID: PMC8089442 DOI: 10.1159/000515344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 11/25/2022]
Abstract
Respiratory and gastrointestinal symptoms are the predominant clinical manifestations of the coronavirus disease 2019 (COVID-19). Infecting intestinal epithelial cells, the severe acute respiratory syndrome coronavirus-2 may impact on host's microbiota and gut inflammation. It is well established that an imbalanced intestinal microbiome can affect pulmonary function, modulating the host immune response ("gut-lung axis"). While effective vaccines and targeted drugs are being tested, alternative pathophysiology-based options to prevent and treat COVID-19 infection must be considered on top of the limited evidence-based therapy currently available. Addressing intestinal dysbiosis with a probiotic supplement may, therefore, be a sensible option to be evaluated, in addition to current best available medical treatments. Herein, we summed up pathophysiologic assumptions and current evidence regarding bacteriotherapy administration in preventing and treating COVID-19 pneumonia.
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Affiliation(s)
- Ornella Spagnolello
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Claudia Pinacchio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Letizia Santinelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paolo Vassalini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Gabriella De Girolamo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- COVID-19 Unit, Azienda Policlinico "Umberto I" University Hospital, Rome, Italy
| | - Silvia Fabris
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Marta Giovanetti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University of Biomedical Campus, Rome, Italy
| | - Alessandro Russo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- COVID-19 Unit, Azienda Policlinico "Umberto I" University Hospital, Rome, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- COVID-19 Unit, Azienda Policlinico "Umberto I" University Hospital, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,
- COVID-19 Unit, Azienda Policlinico "Umberto I" University Hospital, Rome, Italy,
- Migrant and Global Health Research Organization (Mi-HeRo), Rome, Italy,
| | - Gabriella d'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- COVID-19 Unit, Azienda Policlinico "Umberto I" University Hospital, Rome, Italy
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Ceccarelli G, Borrazzo C, Pinacchio C, Santinelli L, Innocenti GP, Cavallari EN, Celani L, Marazzato M, Alessandri F, Ruberto F, Pugliese F, Venditti M, Mastroianni CM, d'Ettorre G. Oral Bacteriotherapy in Patients With COVID-19: A Retrospective Cohort Study. Front Nutr 2021; 7:613928. [PMID: 33505983 PMCID: PMC7829198 DOI: 10.3389/fnut.2020.613928] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Mounting evidence suggests SARS-CoV-2 may impact on host microbiota and gut inflammation, infecting intestinal epithelial cells. This possible link and its implications can be investigated by observing the effects of modulation of the microbial flora in patients with COVID-19. The aim of this study was to compare the rate of mortality, the need of ICU hospitalization and the length of hospitalization in patients with severe COVID-19 pneumonia who received the best available therapy (BAT) vs. patients treated with BAT and supplemented with oral bacteriotherapy. Methods: This retrospective, observational cohort study included 200 adults with severe COVID-19 pneumonia. All patients received therapeutic regimens including low molecular weight heparin plus one or more between hydroxychloroquine, azithromycin, antivirals, and Tocilizumab. Oral bacteriotherapy was used as complementary treatment. Results: Out of the 200 patients, 112 received BAT without oral bacteriotherapy, and 88 BAT with oral bacteriotherapy. Crude mortality was 22%. Eleven percent died in the group of patients treated with BAT plus oral bacteriotherapy vs. 30% subjects in the group of patients managed only with BAT (p < 0.001). By multivariate analysis, the age >65 years, CRP >41.8 mg/L, Platelets <150.000 mmc, and cardiovascular events were associated with the increased risk of mortality. Oral bacteriotherapy was an independent variable associated with a reduced risk for death. Despite large prospective trials are needed, this study highlights a possible role for oral bacteriotherapy in the management of patients hospitalized for COVID-19 pneumonia.
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Affiliation(s)
- Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
| | - Cristian Borrazzo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy.,Medical Statistics Unit, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Claudia Pinacchio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Letizia Santinelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Eugenio Nelson Cavallari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
| | - Luigi Celani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Francesco Alessandri
- Department of Anaesthesia and Intensive Care, Sapienza University of Rome, Rome, Italy
| | - Franco Ruberto
- Department of Anaesthesia and Intensive Care, Sapienza University of Rome, Rome, Italy
| | - Francesco Pugliese
- Department of Anaesthesia and Intensive Care, Sapienza University of Rome, Rome, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
| | - Gabriella d'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Azienda Ospedaliero-Universitaria Policlinico Umberto I, Rome, Italy
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