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Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz JS, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet AH, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, De Vlaminck I. Plasma cell-free RNA signatures of inflammatory syndromes in children. Proc Natl Acad Sci U S A 2024; 121:e2403897121. [PMID: 39240972 DOI: 10.1073/pnas.2403897121] [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: 02/23/2024] [Accepted: 07/25/2024] [Indexed: 09/08/2024] Open
Abstract
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), viral infections, and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C-two conditions presenting with overlapping symptoms-with high performance [test area under the curve = 0.98]. We further extended this methodology into a multiclass machine learning framework that achieved 80% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
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Affiliation(s)
- Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | | | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Joan S Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Emma Belcher
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Will Suslovic
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Meagan E Williams
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
| | - Miriam Oseguera
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Michael A Gardiner
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Jong-Ha Choi
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Hui-Mien Hsiao
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Hao Wang
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Jihoon Kim
- Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06510
| | - Chisato Shimizu
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Meghan Delaney
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
- Department of Pediatrics, George Washington University, School of Medicine & Health Sciences, Washington, DC 20052
| | - Roberta L DeBiasi
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
- Department of Pediatrics, George Washington University, School of Medicine & Health Sciences, Washington, DC 20052
| | - Christina A Rostad
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA 94158
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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Nian Z, Mao Y, Xu Z, Deng M, Xu Y, Xu H, Chen R, Xu Y, Huang N, Mao F, Xu C, Wang Y, Niu M, Chen A, Xue X, Zhang H, Guo G. Multi-omics analysis uncovered systemic lupus erythematosus and COVID-19 crosstalk. Mol Med 2024; 30:81. [PMID: 38862942 PMCID: PMC11167821 DOI: 10.1186/s10020-024-00851-6] [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: 04/01/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Studies have highlighted a possible crosstalk between the pathogeneses of COVID-19 and systemic lupus erythematosus (SLE); however, the interactive mechanisms remain unclear. We aimed to elucidate the impact of COVID-19 on SLE using clinical information and the underlying mechanisms of both diseases. METHODS RNA-seq datasets were used to identify shared hub gene signatures between COVID-19 and SLE, while genome-wide association study datasets were used to delineate the interaction mechanisms of the key signaling pathways. Finally, single-cell RNA-seq datasets were used to determine the primary target cells expressing the shared hub genes and key signaling pathways. RESULTS COVID-19 may affect patients with SLE through hematologic involvement and exacerbated inflammatory responses. We identified 14 shared hub genes between COVID-19 and SLE that were significantly associated with interferon (IFN)-I/II. We also screened and obtained four core transcription factors related to these hub genes, confirming the regulatory role of the IFN-I/II-mediated Janus kinase/signal transducers and activators of transcription (JAK-STAT) signaling pathway on these hub genes. Further, SLE and COVID-19 can interact via IFN-I/II and IFN-I/II receptors, promoting the levels of monokines, including interleukin (IL)-6/10, tumor necrosis factor-α, and IFN-γ, and elevating the incidence rate and risk of cytokine release syndrome. Therefore, in SLE and COVID-19, both hub genes and core TFs are enriched within monocytes/macrophages. CONCLUSIONS The interaction between SLE and COVID-19 promotes the activation of the IFN-I/II-triggered JAK-STAT signaling pathway in monocytes/macrophages. These findings provide a new direction and rationale for diagnosing and treating patients with SLE-COVID-19 comorbidity.
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Affiliation(s)
- Zekai Nian
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Yicheng Mao
- Ophthalmology College, Wenzhou Medical University, Wenzhou, China
| | - Zexia Xu
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ming Deng
- Public Health and Management College, Wenzhou Medical University, Wenzhou, China
| | - Yixi Xu
- School of Public Administration, Hangzhou Normal University, Hangzhou, China
| | - Hanlu Xu
- Ophthalmology College, Wenzhou Medical University, Wenzhou, China
| | - Ruoyao Chen
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Yiliu Xu
- Research Center of Fluid Machinery Engineering and Technology, Jiangsu University, Zhenjiang, China
| | - Nan Huang
- Public Health and Management College, Wenzhou Medical University, Wenzhou, China
| | - Feiyang Mao
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Chenyu Xu
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yulin Wang
- Public Health and Management College, Wenzhou Medical University, Wenzhou, China
| | - Mengyuan Niu
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Aqiong Chen
- Department of Rheumatology, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Huidi Zhang
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
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Heydari R, Tavassolifar MJ, Fayazzadeh S, Sadatpour O, Meyfour A. Long non-coding RNAs in biomarking COVID-19: a machine learning-based approach. Virol J 2024; 21:134. [PMID: 38849961 PMCID: PMC11161961 DOI: 10.1186/s12985-024-02408-9] [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] [Received: 03/19/2024] [Accepted: 06/05/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The coronavirus pandemic that started in 2019 has caused the highest mortality and morbidity rates worldwide. Data on the role of long non-coding RNAs (lncRNAs) in coronavirus disease 2019 (COVID-19) is scarce. We aimed to elucidate the relationship of three important lncRNAs in the inflammatory states, H19, taurine upregulated gene 1 (TUG1), and colorectal neoplasia differentially expressed (CRNDE) with key factors in inflammation and fibrosis induction including signal transducer and activator of transcription3 (STAT3), alpha smooth muscle actin (α-SMA), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in COVID-19 patients with moderate to severe symptoms. METHODS Peripheral blood mononuclear cells from 28 COVID-19 patients and 17 healthy controls were collected. The real-time quantitative polymerase chain reaction (RT-qPCR) was performed to evaluate the expression of RNAs and lncRNAs. Western blotting analysis was also performed to determine the expression levels of STAT3 and α-SMA proteins. Machine learning and receiver operating characteristic (ROC) curve analysis were carried out to evaluate the distinguishing ability of lncRNAs. RESULTS The expression levels of H19, TUG1, and CRNDE were significantly overexpressed in COVID-19 patients compared to healthy controls. Moreover, STAT3 and α-SMA expression levels were remarkedly increased at both transcript and protein levels in patients with COVID-19 compared to healthy subjects and were correlated with Three lncRNAs. Likewise, IL-6 and TNF-α were considerably upregulated in COVID-19 patients. Machine learning and ROC curve analysis showed that CRNDE-H19 panel has the proper ability to distinguish COVID-19 patients from healthy individuals (area under the curve (AUC) = 0.86). CONCLUSION The overexpression of three lncRNAs in COVID-19 patients observed in this study may align with significant manifestations of COVID-19. Furthermore, their co-expression with STAT3 and α-SMA, two critical factors implicated in inflammation and fibrosis induction, underscores their potential involvement in exacerbating cardiovascular, pulmonary and common symptoms and complications associated with COVID-19. The combination of CRNDE and H19 lncRNAs seems to be an impressive host-based biomarker panel for screening and diagnosis of COVID-19 patients from healthy controls. Research into lncRNAs can provide a robust platform to find new viral infection-related mediators and propose novel therapeutic strategies for viral infections and immune disorders.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Tavassolifar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Fayazzadeh
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Omid Sadatpour
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhong P, Bai L, Hong M, Ouyang J, Wang R, Zhang X, Chen P. A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond. Diagnostics (Basel) 2024; 14:1045. [PMID: 38786343 PMCID: PMC11119755 DOI: 10.3390/diagnostics14101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Circulating cfRNA in plasma has emerged as a fascinating area of research with potential applications in disease diagnosis, monitoring, and personalized medicine. Circulating RNA sequencing technology allows for the non-invasive collection of important information about the expression of target genes, eliminating the need for biopsies. This comprehensive review aims to provide a detailed overview of the current knowledge and advancements in the study of plasma cfRNA, focusing on its diverse landscape and biological functions, detection methods, its diagnostic and prognostic potential in various diseases, challenges, and future perspectives.
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Affiliation(s)
- Pengqiang Zhong
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Lu Bai
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Mengzhi Hong
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Juan Ouyang
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Ruizhi Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaoli Zhang
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Peisong Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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Loy C, Cheng MP, Gonzalez-Bocco IH, Lenz J, Belcher E, Bliss A, Eweis-LaBolle D, Chu T, Ritz J, De Vlaminck I. Cell-free RNA Liquid Biopsy to Monitor Hematopoietic Stem Cell Transplantation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307448. [PMID: 38798589 PMCID: PMC11118637 DOI: 10.1101/2024.05.15.24307448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Hematopoietic Stem Cell Transplantation (HSCT) is one of the oldest and most successful immunotherapies. Yet, despite long-standing success in the use of HSCT for the treatment of blood cancers and severe immune disorders, monitoring post-transplant complications remains a challenge due to a lack of informative diagnostic tests. Here, we investigate the utility of cell-free RNA (cfRNA) in plasma as a liquid biopsy to monitor allogeneic HSCT recipients during and after treatment. We assayed longitudinal samples from 92 HSCT recipients by cfRNA sequencing and show that cfRNA provides insight into treatment and recovery trajectories, immune dynamics in response to transplantation, infection, and solid-tissue injury associated with Graft-Versus-Host Disease. Collectively, our results provide support for the use of plasma cfRNA profiling to monitor complications of HSCT.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, 14853, USA
| | - Matthew P. Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Division of Infectious Disease, Brigham and Women’s Hospital; Boston, 02215, USA
| | - Isabel H. Gonzalez-Bocco
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Division of Infectious Disease, Brigham and Women’s Hospital; Boston, 02215, USA
| | - Joan Lenz
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Emma Belcher
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Daniel Eweis-LaBolle
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, 14853, USA
| | - Tinyi Chu
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, 02115, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
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Oliveira TT, Freitas JF, de Medeiros VPB, Xavier TJDS, Agnez-Lima LF. Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity. Life Sci Alliance 2024; 7:e202302358. [PMID: 38262689 PMCID: PMC10806258 DOI: 10.26508/lsa.202302358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
During the COVID-19 pandemic, RNA-seq datasets were produced to investigate the virus-host relationship. However, much of these data remains underexplored. To improve the search for molecular targets and biomarkers, we performed an integrated analysis of multiple RNA-seq datasets, expanding the cohort and including patients from different countries, encompassing severe and mild COVID-19 patients. Our analysis revealed that severe COVID-19 patients exhibit overexpression of genes coding for proteins of extracellular exosomes, endomembrane system, and neutrophil granules (e.g., S100A9, LY96, and RAB1B), which may play an essential role in the cellular response to infection. Concurrently, these patients exhibit down-regulation of genes encoding components of the T cell receptor complex and nucleolus, including TP53, IL2RB, and NCL Finally, SPI1 may emerge as a central transcriptional factor associated with the up-regulated genes, whereas TP53, MYC, and MAX were associated with the down-regulated genes during COVID-19. This study identified targets and transcriptional factors, lighting on the molecular pathophysiology of syndrome coronavirus 2 infection.
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Affiliation(s)
- Thais Teixeira Oliveira
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Júlia Firme Freitas
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | - Thiago Jesus da Silva Xavier
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Lucymara Fassarella Agnez-Lima
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
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Zhang Z, Jin H, Zhang X, Bai M, Zheng K, Tian J, Deng B, Mao L, Qiu P, Huang B. Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression. Front Immunol 2024; 15:1369311. [PMID: 38601162 PMCID: PMC11004287 DOI: 10.3389/fimmu.2024.1369311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Background Coronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses. Methods Sequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes. Results The analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified. Conclusion This research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.
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Affiliation(s)
- Zhen Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Hao Jin
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Xu Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Mei Bai
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Kexin Zheng
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Jing Tian
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bin Deng
- Laboratory Department, Jinzhou Central Hospital, Jinzhou, Liaoning, China
| | - Lingling Mao
- Institute for Prevention and Control of Infection and Infectious Diseases, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Pengcheng Qiu
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bo Huang
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Thoracic Surgery Department, Yingkou Central Hospital, Yingkou, Liaoning, China
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Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz J, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet A, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, Vlaminck ID. Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.06.24303645. [PMID: 38496479 PMCID: PMC10942512 DOI: 10.1101/2024.03.06.24303645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C - two conditions presenting with overlapping symptoms - with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
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Chanda D, Del Rivero T, Ghimire R, More S, Mitrani MI, Bellio MA, Channappanavar R. Acellular Human Amniotic Fluid-Derived Extracellular Vesicles as Novel Anti-Inflammatory Therapeutics against SARS-CoV-2 Infection. Viruses 2024; 16:273. [PMID: 38400048 PMCID: PMC10892347 DOI: 10.3390/v16020273] [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: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 is associated with acute respiratory distress syndrome (ARDS) and fatal pneumonia. Excessive inflammation caused by SARS-CoV-2 is the key driver of ARDS and lethal disease. Several FDA-approved drugs that suppress virus replication are in clinical use. However, despite strong evidence for the role of virus-induced inflammation in severe COVID-19, no effective anti-inflammatory drug is available to control fatal inflammation as well as efficiently clear the virus. Therefore, there is an urgent need to identify biologically derived immunomodulators that suppress inflammation and promote antiviral immunity. In this study, we evaluated acellular human amniotic fluid (acAF) containing extracellular vesicles (hAF-EVs) as a potential non-toxic and safe biologic for immunomodulation during COVID-19. Our in vitro results showed that acAF significantly reduced inflammatory cytokine production in TLR2/4/7 and SARS-CoV-2 structural protein-stimulated mouse macrophages. Importantly, an intraperitoneal administration of acAF reduced morbidity and mortality in SARS-CoV-2-infected mice. A detailed examination of SARS-CoV-2-infected lungs revealed that the increased protection in acAF-treated mice was associated with reduced viral titers and levels of inflammatory myeloid cell infiltration. Collectively, our results identify a novel biologic that has potential to suppress excessive inflammation and enhance survival following SARS-CoV-2 infection, highlighting the translational potential of acAF against COVID-19.
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Affiliation(s)
- Debarati Chanda
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Tania Del Rivero
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Maria Ines Mitrani
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Michael A. Bellio
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Rudragouda Channappanavar
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
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11
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He F, Liu Z, Feng M, Xiao Z, Yi X, Wu J, Liu Z, Wang G, Li L, Yao H. The lncRNA MEG3/miRNA-21/P38MAPK axis inhibits coxsackievirus 3 replication in acute viral myocarditis. Virus Res 2024; 339:199250. [PMID: 37865350 PMCID: PMC10643532 DOI: 10.1016/j.virusres.2023.199250] [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] [Received: 07/14/2023] [Revised: 10/08/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Evidence is emerging on the roles of long noncoding RNAs (lncRNAs) as regulatory factors in a variety of viral infection processes, but the mechanisms underlying their functions in coxsackievirus group B type3 (CVB3)-induced acute viral myocarditis have not been explicitly delineated. We previously demonstrated that CVB3 infection decreases miRNA-21 expression; however, lncRNAs that regulate the miRNA-21-dependent CVB3 disease process have yet to be identified. To evaluate lncRNAs upstream of miRNA-21, differentially expressed lncRNAs in CVB3-infected mouse hearts were identified by microarray analysis and lncRNA/miRNA-21 interactions were predicted bioinformatically. MEG3 was identified as a candidate miRNA-21-interacting lncRNA upregulated in CVB3-infected mouse hearts. MEG3 expression was verified to be upregulated in HeLa cells 48 h post CVB3 infection and to act as a competitive endogenous RNA of miRNA-21. MEG3 knockdown resulted in the upregulation of miRNA-21, which inhibited CVB3 replication by attenuating P38-MAPK signaling in vitro and in vivo. Knockdown of MEG3 expression before CVB3 infection inhibited viral replication in mouse hearts and alleviated cardiac injury, which improved survival. Furthermore, the knockdown of CREB5, which was predicted bioinformatically to function upstream of MEG3, was demonstrated to decrease MEG3 expression and CVB3 viral replication. This study identifies the function of the lncRNA MEG3/miRNA-21/P38 MAPK axis in the process of CVB3 replication, for which CREB5 could serve as an upstream modulator.
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Affiliation(s)
- Feng He
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Zhuo Liu
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Miao Feng
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Zonghui Xiao
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Xiaoyu Yi
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Jianxin Wu
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China; Beijing Municipal Key Laboratory of Child Development and Nutriomics, Beijing, China; Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhewei Liu
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China
| | - Gaoyu Wang
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, China
| | - Le Li
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, China.
| | - Hailan Yao
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, YaBaoRoad 2, Beijing, China.
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12
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Liu X, Xiong W, Ye M, Lu T, Yuan K, Chang S, Han Y, Wang Y, Lu L, Bao Y. Non-coding RNAs expression in SARS-CoV-2 infection: pathogenesis, clinical significance, and therapeutic targets. Signal Transduct Target Ther 2023; 8:441. [PMID: 38057315 PMCID: PMC10700414 DOI: 10.1038/s41392-023-01669-0] [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] [Received: 12/09/2022] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 12/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been looming globally for three years, yet the diagnostic and treatment methods for COVID-19 are still undergoing extensive exploration, which holds paramount importance in mitigating future epidemics. Host non-coding RNAs (ncRNAs) display aberrations in the context of COVID-19. Specifically, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) exhibit a close association with viral infection and disease progression. In this comprehensive review, an overview was presented of the expression profiles of host ncRNAs following SARS-CoV-2 invasion and of the potential functions in COVID-19 development, encompassing viral invasion, replication, immune response, and multiorgan deficits which include respiratory system, cardiac system, central nervous system, peripheral nervous system as well as long COVID. Furthermore, we provide an overview of several promising host ncRNA biomarkers for diverse clinical scenarios related to COVID-19, such as stratification biomarkers, prognostic biomarkers, and predictive biomarkers for treatment response. In addition, we also discuss the therapeutic potential of ncRNAs for COVID-19, presenting ncRNA-based strategies to facilitate the development of novel treatments. Through an in-depth analysis of the interplay between ncRNA and COVID-19 combined with our bioinformatic analysis, we hope to offer valuable insights into the stratification, prognosis, and treatment of COVID-19.
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Affiliation(s)
- Xiaoxing Liu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Wandi Xiong
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Tangsheng Lu
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Kai Yuan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Ying Han
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Yongxiang Wang
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China.
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China.
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
| | - Yanping Bao
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- School of Public Health, Peking University, 100191, Beijing, China.
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13
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Jalaleddine N, Gaudet M, Mogas A, Hachim M, Senok A, Saheb Sharif-Askari N, Mahboub B, Halwani R, Hamid Q, Al Heialy S. Cell free ACE2 RNA: A potential biomarker of COVID-19 severity. Respir Med 2023; 219:107409. [PMID: 37729955 DOI: 10.1016/j.rmed.2023.107409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
Despite the downward trend of COVID-19 pandemic and increased immunity of the general population, COVID-19 is still an elusive disease with risks due to emerging variants. Fast and reliable diagnosis of COVID-19 disease would allow better therapeutic interventions for patients at risk to develop more severe outcomes. Cell-free RNAs (cfRNAs) have been proven to be an effective biomarker in cancer and infectious diseases. It has been reported that cfRNAs are amplified in the bloodstream of these patients and at earlier stages of the disease, reflecting tissue damage. Hence, we hypothesize that cfRNAs may serve as a potential indicator of COVID-19 disease severity. To our knowledge, this is the first report to display a significant link between COVID-19 severity and cfRNA of angiotensin converting enzyme-2 (ACE2), the receptor for SARS-CoV-2 virus. qRT-PCR analysis of liquid biopsies from COVID-19 patients (n = 82) displayed a significant increase in ACE2-cfRNA levels in patients with severe manifestations. This finding correlated with blood biomarkers (ANC, WBC, and Creatinine) that were also significantly increased in these patients. We previously showed that bronchial cells from obese subjects express higher ACE2 levels, hence, we further analysed the involvement of obesity as a main contributor to severe outcomes. We confirm a significant increase of ACE2-cfRNA in the plasma of obese/overweight (Ob/Ov) COVID-19 patients compared to lean subjects, with no observed significant change in blood biomarkers. These findings suggest that monitoring ACE2-cfRNAs, as a biomarker, during COVID-19 infection may allow for better disease management, specifically for severe-COVID-19 patients.
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Affiliation(s)
- Nour Jalaleddine
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mellissa Gaudet
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada
| | - Andrea Mogas
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada
| | - Mahmood Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Bassam Mahboub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Rabih Halwani
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Prince Abdullah Ben Khaled Celiac Disease Research Chair, Department of Paediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates; Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada.
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14
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Greco S, Made' A, Mutoli M, Zhang L, Piella SN, Vausort M, Lumley AI, Beltrami AP, Srivastava PK, Milani V, Boveri S, Ranucci M, Renna LV, Firat H, Bruno A, Spinetti G, Emanueli C, Devaux Y, Martelli F. HCG18, LEF1AS1 and lncCEACAM21 as biomarkers of disease severity in the peripheral blood mononuclear cells of COVID-19 patients. J Transl Med 2023; 21:758. [PMID: 37884975 PMCID: PMC10605335 DOI: 10.1186/s12967-023-04497-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/01/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Even after 3 years from SARS-CoV-2 identification, COVID-19 is still a persistent and dangerous global infectious disease. Significant improvements in our understanding of the disease pathophysiology have now been achieved. Nonetheless, reliable and accurate biomarkers for the early stratification of COVID-19 severity are still lacking. Long noncoding RNAs (LncRNAs) are ncRNAs longer than 200 nucleotides, regulating the transcription and translation of protein-coding genes and they can be found in the peripheral blood, thus holding a promising biomarker potential. Specifically, peripheral blood mononuclear cells (PBMCs) have emerged as a source of indirect biomarkers mirroring the conditions of tissues: they include monocytes, B and T lymphocytes, and natural killer T cells (NKT), being highly informative for immune-related events. METHODS We profiled by RNA-Sequencing a panel of 2906 lncRNAs to investigate their modulation in PBMCs of a pilot group of COVID-19 patients, followed by qPCR validation in 111 hospitalized COVID-19 patients. RESULTS The levels of four lncRNAs were found to be decreased in association with COVID-19 mortality and disease severity: HLA Complex Group 18-242 and -244 (HCG18-242 and HCG18-244), Lymphoid Enhancer Binding Factor 1-antisense 1 (LEF1-AS1) and lncCEACAM21 (i.e. ENST00000601116.5, a lncRNA in the CEACAM21 locus). Interestingly, these deregulations were confirmed in an independent patient group of hospitalized patients and by the re-analysis of publicly available single-cell transcriptome datasets. The identified lncRNAs were expressed in all of the PBMC cell types and inversely correlated with the neutrophil/lymphocyte ratio (NLR), an inflammatory marker. In vitro, the expression of LEF1-AS1 and lncCEACAM21 was decreased upon THP-1 monocytes exposure to a relevant stimulus, hypoxia. CONCLUSION The identified COVID-19-lncRNAs are proposed as potential innovative biomarkers of COVID-19 severity and mortality.
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Affiliation(s)
- Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy.
| | - Alisia Made'
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy
| | - Martina Mutoli
- IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, Italy
| | - Lu Zhang
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Santiago Nicolas Piella
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy
| | - Mélanie Vausort
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Andrew I Lumley
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | | | - Prashant Kumar Srivastava
- National Heart and Lung Institute, Imperial College London, Hammersmith Campus, London, W12 0NN, England, UK
| | - Valentina Milani
- Laboratory of Biostatistics and Data Management, Scientific Directorate, IRCCS Policlinico San Donato, 20097, San Donato Milanese, Milan, Italy
| | - Sara Boveri
- Laboratory of Biostatistics and Data Management, Scientific Directorate, IRCCS Policlinico San Donato, 20097, San Donato Milanese, Milan, Italy
| | - Marco Ranucci
- Department of Cardiovascular Anesthesia and ICU, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy
| | - Laura Valentina Renna
- Biobank BioCor, IRCCS-Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy
| | | | - Antonino Bruno
- IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, Italy
- Laboratory of Immunology and General Pathology, Department of Biotechnology and Life Sciences, University of Insubria, Via Monte Generoso 71, 21100, Varese, Italy
| | - Gaia Spinetti
- IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, Italy
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, Hammersmith Campus, London, W12 0NN, England, UK.
- National Heart & Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK.
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445, Strassen, Luxembourg.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, Milan, Italy.
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15
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Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
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Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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16
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Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep Med 2023; 4:101034. [PMID: 37279751 PMCID: PMC10121104 DOI: 10.1016/j.xcrm.2023.101034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/28/2022] [Accepted: 04/11/2023] [Indexed: 06/08/2023]
Abstract
Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here, we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with COVID-19 or MIS-C across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multiorgan involvement in MIS-C encompassing diverse cell types, including endothelial and neuronal cells, and an enrichment of pyroptosis-related genes. Whole-blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C but also MIS-C-specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole-blood RNA in paired samples yields different but complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs future development of new disease biomarkers.
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Affiliation(s)
- Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joan Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Sanchita Bhattacharya
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Alexandre P Cheng
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte J Hsieh
- Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California San Francisco, Oakland, CA 94609
| | - Burak Bahar
- Children's National Hospital, Washington, DC 20010, USA
| | - Nathan Wood
- UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kushmita Bhakta
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Maria A Perez
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Laila Hussaini
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Evan J Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Meghan Delaney
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roberta L DeBiasi
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
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17
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Li J, Ren J, Liao H, Guo W, Feng K, Huang T, Cai YD. Identification of dynamic gene expression profiles during sequential vaccination with ChAdOx1/BNT162b2 using machine learning methods. Front Microbiol 2023; 14:1138674. [PMID: 37007526 PMCID: PMC10063797 DOI: 10.3389/fmicb.2023.1138674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/01/2023] [Indexed: 03/19/2023] Open
Abstract
To date, COVID-19 remains a serious global public health problem. Vaccination against SARS-CoV-2 has been adopted by many countries as an effective coping strategy. The strength of the body’s immune response in the face of viral infection correlates with the number of vaccinations and the duration of vaccination. In this study, we aimed to identify specific genes that may trigger and control the immune response to COVID-19 under different vaccination scenarios. A machine learning-based approach was designed to analyze the blood transcriptomes of 161 individuals who were classified into six groups according to the dose and timing of inoculations, including I-D0, I-D2-4, I-D7 (day 0, days 2–4, and day 7 after the first dose of ChAdOx1, respectively) and II-D0, II-D1-4, II-D7-10 (day 0, days 1–4, and days 7–10 after the second dose of BNT162b2, respectively). Each sample was represented by the expression levels of 26,364 genes. The first dose was ChAdOx1, whereas the second dose was mainly BNT162b2 (Only four individuals received a second dose of ChAdOx1). The groups were deemed as labels and genes were considered as features. Several machine learning algorithms were employed to analyze such classification problem. In detail, five feature ranking algorithms (Lasso, LightGBM, MCFS, mRMR, and PFI) were first applied to evaluate the importance of each gene feature, resulting in five feature lists. Then, the lists were put into incremental feature selection method with four classification algorithms to extract essential genes, classification rules and build optimal classifiers. The essential genes, namely, NRF2, RPRD1B, NEU3, SMC5, and TPX2, have been previously associated with immune response. This study also summarized expression rules that describe different vaccination scenarios to help determine the molecular mechanism of vaccine-induced antiviral immunity.
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Affiliation(s)
- Jing Li
- School of Computer Science, Baicheng Normal University, Baicheng, Jilin, China
| | - JingXin Ren
- School of Life Sciences, Shanghai University, Shanghai, China
| | | | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
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18
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Lei H. A two-gene marker for the two-tiered innate immune response in COVID-19 patients. PLoS One 2023; 18:e0280392. [PMID: 36649304 PMCID: PMC9844909 DOI: 10.1371/journal.pone.0280392] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
For coronavirus disease 2019 (COVID-19), a pandemic disease characterized by strong immune dysregulation in severe patients, convenient and efficient monitoring of the host immune response is critical. Human hosts respond to viral and bacterial infections in different ways, the former is characterized by the activation of interferon stimulated genes (ISGs) such as IFI27, while the latter is characterized by the activation of anti-bacterial associated genes (ABGs) such as S100A12. This two-tiered innate immune response has not been examined in COVID-19. In this study, the activation patterns of this two-tiered innate immune response represented by IFI27 and S100A12 were explored based on 1421 samples from 17 transcriptome datasets derived from the blood of COVID-19 patients and relevant controls. It was found that IFI27 activation occurred in most of the symptomatic patients and displayed no correlation with disease severity, while S100A12 activation was more restricted to patients under severe and critical conditions with a stepwise activation pattern. In addition, most of the S100A12 activation was accompanied by IFI27 activation. Furthermore, the activation of IFI27 was most pronounced within the first week of symptom onset, but generally waned after 2-3 weeks. On the other hand, the activation of S100A12 displayed no apparent correlation with disease duration and could last for several months in certain patients. These features of the two-tiered innate immune response can further our understanding on the disease mechanism of COVID-19 and may have implications to the clinical triage. Development of a convenient two-gene protocol for the routine serial monitoring of this two-tiered immune response will be a valuable addition to the existing laboratory tests.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- Cunji Medical School, University of Chinese Academy of Sciences, Beijing, China
- Center of Alzheimer’s Disease, Beijing Institute for Brain Disorders, Beijing, China
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19
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Shojaei M, Shamshirian A, Monkman J, Grice L, Tran M, Tan CW, Teo SM, Rodrigues Rossi G, McCulloch TR, Nalos M, Raei M, Razavi A, Ghasemian R, Gheibi M, Roozbeh F, Sly PD, Spann KM, Chew KY, Zhu Y, Xia Y, Wells TJ, Senegaglia AC, Kuniyoshi CL, Franck CL, dos Santos AFR, de Noronha L, Motamen S, Valadan R, Amjadi O, Gogna R, Madan E, Alizadeh-Navaei R, Lamperti L, Zuñiga F, Nova-Lamperti E, Labarca G, Knippenberg B, Herwanto V, Wang Y, Phu A, Chew T, Kwan T, Kim K, Teoh S, Pelaia TM, Kuan WS, Jee Y, Iredell J, O’Byrne K, Fraser JF, Davis MJ, Belz GT, Warkiani ME, Gallo CS, Souza-Fonseca-Guimaraes F, Nguyen Q, Mclean A, Kulasinghe A, Short KR, Tang B. IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study. Front Immunol 2023; 13:1060438. [PMID: 36685600 PMCID: PMC9850159 DOI: 10.3389/fimmu.2022.1060438] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023] Open
Abstract
Purpose Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate biomarkers have been proposed for COVID-19. However, at present, there is no consensus on the best diagnostic approach to predict outcomes in infected patients. Moreover, it is not clear whether such tools would apply to other potentially pandemic pathogens and therefore of use as stockpile for future pandemic preparedness. Methods We conducted a multi-cohort observational study to investigate the biology and the prognostic role of interferon alpha-inducible protein 27 (IFI27) in COVID-19 patients. Results We show that IFI27 is expressed in the respiratory tract of COVID-19 patients and elevated IFI27 expression in the lower respiratory tract is associated with the presence of a high viral load. We further demonstrate that the systemic host response, as measured by blood IFI27 expression, is associated with COVID-19 infection. For clinical outcome prediction (e.g., respiratory failure), IFI27 expression displays a high sensitivity (0.95) and specificity (0.83), outperforming other known predictors of COVID-19 outcomes. Furthermore, IFI27 is upregulated in the blood of infected patients in response to other respiratory viruses. For example, in the pandemic H1N1/09 influenza virus infection, IFI27-like genes were highly upregulated in the blood samples of severely infected patients. Conclusion These data suggest that prognostic biomarkers targeting the family of IFI27 genes could potentially supplement conventional diagnostic tools in future virus pandemics, independent of whether such pandemics are caused by a coronavirus, an influenza virus or another as yet-to-be discovered respiratory virus.
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Affiliation(s)
- Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Amir Shamshirian
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Grice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Siok Min Teo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gustavo Rodrigues Rossi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy R. McCulloch
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Marek Nalos
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Maedeh Raei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Roya Ghasemian
- Antimicrobial Resistance Research Centre, Department of Infectious Diseases, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mobina Gheibi
- Student Research Committee, School of Allied Medical Sciences, Mazandaran University of Medical Science, Sari, Iran
| | | | - Peter D. Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, QLD, Australia
| | - Kirsten M. Spann
- Centre for Immunology and Infection Control, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yao Xia
- School of Science, Edith Cowan University; School of Biomedical Science, University of Western Australia, Perth, WA, Australia
| | - Timothy J. Wells
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Alexandra Cristina Senegaglia
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | - Carmen Lúcia Kuniyoshi
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | | | | | | | - Sepideh Motamen
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza Valadan
- Molecular and Cell Biology Research Centre, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran,Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Omolbanin Amjadi
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rajan Gogna
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark,Novo Nordisk Foundation centre for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Esha Madan
- Campania Centre for the Unknown, Lisbon, Portugal
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Liliana Lamperti
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile
| | - Felipe Zuñiga
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Gonzalo Labarca
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Faculty of Medicine, Universidad de Concepcion, Concepcion, Chile
| | - Ben Knippenberg
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Velma Herwanto
- Faculty of Medicine, Universitas Tarumanagara, Jakarta, Indonesia
| | - Ya Wang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia
| | - Amy Phu
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Westmead Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Tracy Chew
- Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, NSW, Australia
| | - Timothy Kwan
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Karan Kim
- Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Tiana M. Pelaia
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Win Sen Kuan
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yvette Jee
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore
| | - Jon Iredell
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW, Australia,Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Ken O’Byrne
- Queensland University of Technology, Centre for Genomics and PersonalisedHealth, School of Biomedical Sciences, Brisbane, QLD, Australia
| | - John F. Fraser
- Critical Care Research Group, The University of Queensland, Brisbane, QLD, Australia
| | - Melissa J. Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Gabrielle T. Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Majid E. Warkiani
- Australia Centre for Health Technologies (CHT) & Institute for Biomedical Materials & Devices (IBMD), School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Carlos Salomon Gallo
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, The University of Queensland, Brisbane, QLD, Australia
| | | | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anthony Mclean
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
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20
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Sun Z, Ke L, Zhao Q, Qu J, Hu Y, Gao H, Peng Z. The use of bioinformatics methods to identify the effects of SARS-CoV-2 and influenza viruses on the regulation of gene expression in patients. Front Immunol 2023; 14:1098688. [PMID: 36911695 PMCID: PMC9992716 DOI: 10.3389/fimmu.2023.1098688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Background SARS-CoV-2 infection is a respiratory infectious disease similar to influenza virus infection. Numerous studies have reported similarities and differences in the clinical manifestations, laboratory tests, and mortality between these two infections. However, the genetic effects of coronavirus and influenza viruses on the host that lead to these characteristics have rarely been reported. Methods COVID-19 (GSE157103) and influenza (GSE111368, GSE101702) datasets were downloaded from the Gene Expression Ominbus (GEO) database. Differential gene, gene set enrichment, protein-protein interaction (PPI) network, gene regulatory network, and immune cell infiltration analyses were performed to identify the critical impact of COVID-19 and influenza viruses on the regulation of host gene expression. Results The number of differentially expressed genes in the COVID-19 patients was significantly higher than in the influenza patients. 22 common differentially expressed genes (DEGs) were identified between the COVID-19 and influenza datasets. The effects of the viruses on the regulation of host gene expression were determined using gene set enrichment and PPI network analyses. Five HUB genes were finally identified: IFI27, OASL, RSAD2, IFI6, and IFI44L. Conclusion We identified five HUB genes between COVID-19 and influenza virus infection, which might be helpful in the diagnosis and treatment of COVID-19 and influenza. This knowledge may also guide future mechanistic studies that aim to identify pathogen-specific interventions.
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Affiliation(s)
- Zhongyi Sun
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
| | - Li Ke
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
| | - Qiuyue Zhao
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
| | - Jiachen Qu
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
| | - Yanan Hu
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
| | - Han Gao
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhiyong Peng
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Clinical Research Center of Hubei Critical Care Medicine, Wuhan, Hubei, China
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21
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Chaddha M, Rai H, Gupta R, Thakral D. Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment. Front Genet 2023; 14:1138625. [PMID: 37091783 PMCID: PMC10117686 DOI: 10.3389/fgene.2023.1138625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
The circulating cell-free nucleic acids (ccfNAs) consist of a heterogenous cocktail of both single (ssNA) and double-stranded (dsNA) nucleic acids. These ccfNAs are secreted into the blood circulation by both healthy and malignant cells via various mechanisms including apoptosis, necrosis, and active secretion. The major source of ccfNAs are the cells of hematopoietic system under healthy conditions. These ccfNAs include fragmented circulating cell free DNA (ccfDNA), coding or messenger RNA (mRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and mitochondrial DNA/RNA (mtDNA and mtRNA), that serve as prospective biomarkers in assessment of various clinical conditions. For, e.g., free fetal DNA and RNA migrate into the maternal plasma, whereas circulating tumor DNA (ctDNA) has clinical relevance in diagnostic, prognostic, therapeutic targeting, and disease progression monitoring to improve precision medicine in cancer. The epigenetic modifications of ccfDNA as well as circulating cell-free RNA (ccfRNA) such as miRNA and lncRNA show disease-related variations and hold potential as epigenetic biomarkers. The messenger RNA present in the circulation or the circulating cell free mRNA (ccf-mRNA) and long non-coding RNA (ccf-lncRNA) have gradually become substantial in liquid biopsy by acting as effective biomarkers to assess various aspects of disease diagnosis and prognosis. Conversely, the simultaneous characterization of coding and non-coding RNAs in human biofluids still poses a significant hurdle. Moreover, a comprehensive assessment of ccfRNA that may reflect the tumor microenvironment is being explored. In this review, we focus on the novel approaches for exploring ccfDNA and ccfRNAs, specifically ccf-mRNA as biomarkers in clinical diagnosis and prognosis of cancer. Integrating the detection of circulating tumor DNA (ctDNA) for cancer genotyping in conjunction with ccfRNA both quantitatively and qualitatively, may potentially hold immense promise towards precision medicine. The current challenges and future directions in deciphering the complexity of cancer networks based on the dynamic state of ccfNAs will be discussed.
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Affiliation(s)
| | | | - Ritu Gupta
- *Correspondence: Deepshi Thakral, ; Ritu Gupta,
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22
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Sun Y, Wang M, Lin W, Dong W, Xu J. Massive-scale genomic analysis reveals SARS-CoV-2 mutation characteristics and evolutionary trends. MLIFE 2022; 1:311-322. [PMID: 37732331 PMCID: PMC9538474 DOI: 10.1002/mlf2.12040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/05/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic resulted in significant societal costs. Hence, an in-depth understanding of SARS-CoV-2 virus mutation and its evolution will help determine the direction of the COVID-19 pandemic. In this study, we identified 296,728 de novo mutations in more than 2,800,000 high-quality SARS-CoV-2 genomes. All possible factors affecting the mutation frequency of SARS-CoV-2 in human hosts were analyzed, including zinc finger antiviral proteins, sequence context, amino acid change, and translation efficiency. As a result, we proposed that when adenine (A) and tyrosine (T) bases are in the context of AM (M stands for adenine or cytosine) or TA motif, A or T base has lower mutation frequency. Furthermore, we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection, which explains why SARS-CoV-2 prefers AT3 codons usage. In addition, we found a host-specific asymmetric dinucleotide mutation frequency in the SARS-CoV-2 genome, which provides a new basis for determining the origin of the SARS-CoV-2. Finally, we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS-CoV-2.
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Affiliation(s)
- Yamin Sun
- Research Institute of Public HealthNankai UniversityTianjinChina
| | - Min Wang
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjinChina
- Engineering and Research Center for Microbial Functional Genomics and Detection, Ministry of EducationNankai UniversityTianjinChina
| | - Wenchao Lin
- Engineering and Research Center for Microbial Functional Genomics and Detection, Ministry of EducationNankai UniversityTianjinChina
| | - Wei Dong
- Engineering and Research Center for Microbial Functional Genomics and Detection, Ministry of EducationNankai UniversityTianjinChina
| | - Jianguo Xu
- Research Institute of Public HealthNankai UniversityTianjinChina
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and PreventionNational Institute for Communicable Disease Control and PreventionBeijingChina
- Research Units of Discovery of Unknown Bacteria and FunctionChinese Academy of Medical SciencesBeijingChina
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23
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Cabús L, Lagarde J, Curado J, Lizano E, Pérez-Boza J. Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res 2022; 10:62. [PMID: 35978416 PMCID: PMC9385245 DOI: 10.1186/s40364-022-00409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
The analysis of biomarkers in biological fluids, also known as liquid biopsies, is seen with great potential to diagnose complex diseases such as cancer with a high sensitivity and minimal invasiveness. Although it can target any biomolecule, most liquid biopsy studies have focused on circulating nucleic acids. Historically, studies have aimed at the detection of specific mutations on cell-free DNA (cfDNA), but recently, the study of cell-free RNA (cfRNA) has gained traction. Since 2020, a handful of cfDNA tests have been approved for therapy selection by the FDA, however, no cfRNA tests are approved to date. One of the main drawbacks in the field of RNA-based liquid biopsies is the low reproducibility of the results, often caused by technical and biological variability, a lack of standardized protocols and insufficient cohorts. In this review, we will identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cfRNA and propose solutions to minimize them.
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Affiliation(s)
- Lluc Cabús
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
- Flomics Biotech, Barcelona, Spain
| | | | | | - Esther Lizano
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
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24
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Zhong Y, Ashley CL, Steain M, Ataide SF. Assessing the suitability of long non-coding RNAs as therapeutic targets and biomarkers in SARS-CoV-2 infection. Front Mol Biosci 2022; 9:975322. [PMID: 36052163 PMCID: PMC9424846 DOI: 10.3389/fmolb.2022.975322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts that are over 200 nucleotides and rarely encode proteins or peptides. They regulate gene expression and protein activities and are heavily involved in many cellular processes such as cytokine secretion in respond to viral infection. In severe COVID-19 cases, hyperactivation of the immune system may cause an abnormally sharp increase in pro-inflammatory cytokines, known as cytokine release syndrome (CRS), which leads to severe tissue damage or even organ failure, raising COVID-19 mortality rate. In this review, we assessed the correlation between lncRNAs expression and cytokine release syndrome by comparing lncRNA profiles between COVID-19 patients and health controls, as well as between severe and non-severe cases. We also discussed the role of lncRNAs in CRS contributors and showed that the lncRNA profiles display consistency with patients’ clinic symptoms, thus suggesting the potential of lncRNAs as drug targets or biomarkers in COVID-19 treatment.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Caroline L. Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sandro Fernandes Ataide
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Sandro Fernandes Ataide,
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Liu Z, Wang T, Yang X, Zhou Q, Zhu S, Zeng J, Chen H, Sun J, Li L, Xu J, Geng C, Xu X, Wang J, Yang H, Zhu S, Chen F, Wang W. Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids. Clin Transl Med 2022; 12:e987. [PMID: 35858042 PMCID: PMC9299576 DOI: 10.1002/ctm2.987] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Cell-free messenger RNA (cf-mRNA) and long non-coding RNA (cf-lncRNA) are becoming increasingly important in liquid biopsy by providing biomarkers for disease prediction, diagnosis and prognosis, but the simultaneous characterization of coding and non-coding RNAs in human biofluids remains challenging. METHODS Here, we developed polyadenylation ligation-mediated sequencing (PALM-Seq), an RNA sequencing strategy employing treatment of RNA with T4 polynucleotide kinase to generate cell-free RNA (cfRNA) fragments with 5' phosphate and 3' hydroxyl and RNase H to deplete abundant RNAs, achieving simultaneous quantification and characterization of cfRNAs. RESULTS Using PALM-Seq, we successfully identified well-known differentially abundant mRNA, lncRNA and microRNA in the blood plasma of pregnant women. We further characterized cfRNAs in blood plasma, saliva, urine, seminal plasma and amniotic fluid and found that the detected numbers of different RNA biotypes varied with body fluids. The profiles of cf-mRNA reflected the function of originated tissues, and immune cells significantly contributed RNA to blood plasma and saliva. Short fragments (<50 nt) of mRNA and lncRNA were major in biofluids, whereas seminal plasma and amniotic fluid tended to retain long RNA. Body fluids showed distinct preferences of pyrimidine at the 3' end and adenine at the 5' end of cf-mRNA and cf-lncRNA, which were correlated with the proportions of short fragments. CONCLUSION Together, PALM-Seq enables a simultaneous characterization of cf-mRNA and cf-lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.
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Affiliation(s)
| | | | | | | | - Sujun Zhu
- Obstetrics DepartmentShenzhen Maternity and Child Healthcare HospitalShenzhenGuangdong ProvinceChina
| | - Juan Zeng
- Obstetrics DepartmentShenzhen Maternity and Child Healthcare HospitalShenzhenGuangdong ProvinceChina
| | | | - Jinghua Sun
- BGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | | | - Xun Xu
- BGI‐ShenzhenShenzhenChina
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Yang CY, Chen YH, Liu PJ, Hu WC, Lu KC, Tsai KW. The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection. Int J Med Sci 2022; 19:1340-1356. [PMID: 35928726 PMCID: PMC9346380 DOI: 10.7150/ijms.76168] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause immunosuppression and cytokine storm, leading to lung damage and death. The clinical efficacy of anti-SARS-CoV-2 drugs in preventing viral entry into host cells and suppressing viral replication remains inadequate. MicroRNAs (miRNAs) are crucial to the immune response to and pathogenesis of coronaviruses, such as SARS-CoV-2. However, the specific roles of miRNAs in the life cycle of SARS-CoV-2 remain unclear. miRNAs can participate in SARS-CoV-2 infection and pathogenesis through at least four possible mechanisms: 1. host cell miRNA expression interfering with SARS-CoV-2 cell entry, 2. SARS-CoV-2-derived RNA transcripts acting as competitive endogenous RNAs (ceRNAs) that may attenuate host cell miRNA expression, 3. host cell miRNA expression modulating SARS-CoV-2 replication, and 4. SARS-CoV-2-encoded miRNAs silencing the expression of host protein-coding genes. SARS-CoV-2-related miRNAs may be used as diagnostic or prognostic biomarkers for predicting outcomes among patients with SARS-CoV-2 infection. Furthermore, accumulating evidence suggests that dietary polyphenolic compounds may protect against SARS-CoV-2 infection by modulating host cell miRNA expression. These findings have major implications for the future diagnosis and treatment of COVID-19.
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Affiliation(s)
- Chih-Yun Yang
- Division of Chest Medicine, Kaohsiung Municipal Min-Sheng Hospital, Kaohsiung, Taiwan, ROC
| | - Yu-Hsuan Chen
- Division of Chest Medicine, Department of Internal Medicine, CHENG HSIN General Hospital, Taipei, Taiwan, ROC
| | - Pei-Jung Liu
- Division of Chest Medicine, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Chung Hu
- Department of Clinical Pathology and Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC.,Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan, ROC
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
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