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Regina Malveste Ito C, Santos MO, de Oliveira Cunha M, de Araújo KM, de Souza GRL, Rézio GS, de Brito PN, Rezende APC, Fonseca JG, Wastowski IJ, Gonçalves Vieira JD, Gomes Avelino MA, Carneiro LC. Rhinovirus infection and co-infection in children with severe acute respiratory infection during the COVID-19 pandemic period. Virulence 2024; 15:2310873. [PMID: 38384141 PMCID: PMC10885176 DOI: 10.1080/21505594.2024.2310873] [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: 06/11/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Rhinovirus causes respiratory tract infections in children and is found in co-infections. The objective of this research was to study the clinical profile of rhinovirus infection and co-infection in children with severe acute respiratory infection (SARI) during the COVID-19 pandemic period. We included 606 children ranging in age from 0.1 to 144 months of age from March 2020 to December 2021, hospitalized in the Pediatric Intensive Care Unit (PICU). The samples were collected by secretion from the nasopharynx region. A total of 259 children were tested positive for viral infection, 153 (59.07%) of them had a single rhinovirus infection and, 56 (36.6%) were aged between 60.1 and 144 months. Nine types of co-infections were identified and were found coinfection with three or more viruses (22/104, 21.15%). Observing the seasonality, the number of cases was similar between 2020 (49.53%) and 2021 (51.47%). Patients with a single infection (86.88%) and coinfection (67.30%) were more likely to have coughed. Patients with co-infection required the use of O2 for longer than those with a single rhinovirus infection. Hemogram results obtained from individuals with a single infection had higher levels of urea when compared to patients with co-infection with and other respiratory viruses. Multiple correspondence analyses indicated different clinical symptoms and comorbidities in patients with co-infection compared to those with single infection. The results found that the rhinovirus was much prevalent virus during the pandemic period and was found in co-infection with other virus types, what is important to diagnostic for the correct treatment of patients.
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Affiliation(s)
- Célia Regina Malveste Ito
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Mônica Oliveira Santos
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Marcos de Oliveira Cunha
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Kelliane Martins de Araújo
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Guilherme Rocha Lino de Souza
- Biochemistry and Molecular Biology Laboratory, Biologic Science Institute, Federal University of Goiás, Samambaia Camp, Goiânia, Goiás, Brazil
| | - Geovana Sôffa Rézio
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Pollyanna Neta de Brito
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Alana Parreira Costa Rezende
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Jakeline Godinho Fonseca
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Isabela Jubé Wastowski
- Molecular Immunology Laboratory of Goiás State University, Laranjeiras Unity Prof. Alfredo de Castro neighborhood, Goiânia, Goiás, Brazil
| | - José Daniel Gonçalves Vieira
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Melissa Ameloti Gomes Avelino
- Department of Pediatrics, Federal University of Goiás, Universitaria Avenue, Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Lilian Carla Carneiro
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás– 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
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Blood leukocyte transcriptional modules and differentially expressed genes associated with disease severity and age in COVID-19 patients. Sci Rep 2023; 13:898. [PMID: 36650374 PMCID: PMC9844197 DOI: 10.1038/s41598-023-28227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Since the molecular mechanisms determining COVID-19 severity are not yet well understood, there is a demand for biomarkers derived from comparative transcriptome analyses of mild and severe cases, combined with patients' clinico-demographic and laboratory data. Here the transcriptomic response of human leukocytes to SARS-CoV-2 infection was investigated by focusing on the differences between mild and severe cases and between age subgroups (younger and older adults). Three transcriptional modules correlated with these traits were functionally characterized, as well as 23 differentially expressed genes (DEGs) associated to disease severity. One module, correlated with severe cases and older patients, had an overrepresentation of genes involved in innate immune response and in neutrophil activation, whereas two other modules, correlated with disease severity and younger patients, harbored genes involved in the innate immune response to viral infections, and in the regulation of this response. This transcriptomic mechanism could be related to the better outcome observed in younger COVID-19 patients. The DEGs, all hyper-expressed in the group of severe cases, were mostly involved in neutrophil activation and in the p53 pathway, therefore related to inflammation and lymphopenia. These biomarkers may be useful for getting a better stratification of risk factors in COVID-19.
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Gallego-Paez LM, Mauer J. DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization. FRONTIERS IN BIOINFORMATICS 2022; 2:786898. [PMID: 36304260 PMCID: PMC9580925 DOI: 10.3389/fbinf.2022.786898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
RNA-seq analysis of alternative pre-mRNA splicing has facilitated an unprecedented understanding of transcriptome complexity in health and disease. However, despite the availability of countless bioinformatic pipelines for transcriptome-wide splicing analysis, the use of these tools is often limited to expert bioinformaticians. The need for high computational power, combined with computational outputs that are complicated to visualize and interpret present obstacles to the broader research community. Here we introduce DJExpress, an R package for differential expression analysis of transcriptomic features and expression-trait associations. To determine gene-level differential junction usage as well as associations between junction expression and molecular/clinical features, DJExpress uses raw splice junction counts as input data. Importantly, DJExpress runs on an average laptop computer and provides a set of interactive and intuitive visualization formats. In contrast to most existing pipelines, DJExpress can handle both annotated and de novo identified splice junctions, thereby allowing the quantification of novel splice events. Moreover, DJExpress offers a web-compatible graphical interface allowing the analysis of user-provided data as well as the visualization of splice events within our custom database of differential junction expression in cancer (DJEC DB). DJEC DB includes not only healthy and tumor tissue junction expression data from TCGA and GTEx repositories but also cancer cell line data from the DepMap project. The integration of DepMap functional genomics data sets allows association of junction expression with molecular features such as gene dependencies and drug response profiles. This facilitates identification of cancer cell models for specific splicing alterations that can then be used for functional characterization in the lab. Thus, DJExpress represents a powerful and user-friendly tool for exploration of alternative splicing alterations in RNA-seq data, including multi-level data integration of alternative splicing signatures in healthy tissue, tumors and cancer cell lines.
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Affiliation(s)
| | - Jan Mauer
- *Correspondence: Lina Marcela Gallego-Paez, ; Jan Mauer,
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Zhang YH, Li Z, Zeng T, Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One 2021; 16:e0250032. [PMID: 33886611 PMCID: PMC8062050 DOI: 10.1371/journal.pone.0250032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Pregnancy is a complicated and long procedure during one or more offspring development inside a woman. A short period of oxygen shortage after birth is quite normal for most babies and does not threaten their health. However, if babies have to suffer from a long period of oxygen shortage, then this condition is an indication of pathological fetal intolerance, which probably causes their death. The identification of the pathological fetal intolerance from the physical oxygen shortage is one of the important clinical problems in obstetrics for a long time. The clinical syndromes typically manifest five symptoms that indicate that the baby may suffer from fetal intolerance. At present, liquid biopsy combined with high-throughput sequencing or mass spectrum techniques provides a quick approach to detect real-time alteration in the peripheral blood at multiple levels with the rapid development of molecule sequencing technologies. Gene methylation is functionally correlated with gene expression; thus, the combination of gene methylation and expression information would help in screening out the key regulators for the pathogenesis of fetal intolerance. We combined gene methylation and expression features together and screened out the optimal features, including gene expression or methylation signatures, for fetal intolerance prediction for the first time. In addition, we applied various computational methods to construct a comprehensive computational pipeline to identify the potential biomarkers for fetal intolerance dependent on the liquid biopsy samples. We set up qualitative and quantitative computational models for the prediction for fetal intolerance during pregnancy. Moreover, we provided a new prospective for the detailed pathological mechanism of fetal intolerance. This work can provide a solid foundation for further experimental research and contribute to the application of liquid biopsy in antenatal care.
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Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Margarita Gamarra
- Department of Computational Science and Electronic, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Romany F. Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga, Egypt
| | - José Escorcia-Gutierrez
- Electronic and Telecommunicacions Program, Universidad Autónoma del Caribe, Barranquilla, Colombia
- * E-mail: (JEG); (TH); (YDC)
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 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
- * E-mail: (JEG); (TH); (YDC)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
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Johnston D, Earley B, McCabe MS, Kim J, Taylor JF, Lemon K, McMenamy M, Duffy C, Cosby SL, Waters SM. Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus. Front Genet 2021; 12:633125. [PMID: 33968129 PMCID: PMC8100685 DOI: 10.3389/fgene.2021.633125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting cattle of all ages. One of the main causes of BRD is an initial inflammatory response to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging non-coding small RNAs that regulate many biological processes and are implicated in various inflammatory diseases. The objective of the present study was to elucidate the changes in the bovine bronchial lymph node miRNA transcriptome in response to BRSV following an experimental viral challenge. Holstein-Friesian calves were either administered a challenge dose of BRSV (103.5 TCID50/ml × 15 ml) (n = 12) or were mock inoculated with sterile phosphate buffered saline (n = 6). Daily scoring of clinical signs was performed and calves were euthanized at day 7 post-challenge. Bronchial lymph nodes were collected for subsequent RNA extraction and sequencing (75 bp). Read counts for known miRNAs were generated using the miRDeep2 package using the UMD3.1 reference genome and the bovine mature miRNA sequences from the miRBase database (release 22). EdgeR was used for differential expression analysis and Targetscan was used to identify target genes for the differentially expressed (DE) miRNAs. Target genes were examined for enriched pathways and gene ontologies using Ingenuity Pathway Analysis (Qiagen). Multi-dimensional scaling (MDS) based on miRNA gene expression changes, revealed a clearly defined separation between the BRSV challenged and control calves, although the clinical manifestation of disease was only mild. One hundred and nineteen DE miRNAs (P < 0.05, FDR < 0.1, fold change > 1.5) were detected between the BRSV challenged and control calves. The DE miRNAs were predicted to target 465 genes which were previously found to be DE in bronchial lymph node tissue, between these BRSV challenged and control calves. Of the DE predicted target genes, 455 had fold changes that were inverse to the corresponding DE miRNAs. There were eight enriched pathways among the DE predicted target genes with inverse fold changes to their corresponding DE miRNA including: granulocyte and agranulocyte adhesion and diapedesis, interferon signalling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be increased included: T cell response, apoptosis of leukocytes, immune response of cells and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are vital for the recognition of the virus and its subsequent elimination.
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Affiliation(s)
- Dayle Johnston
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Ireland
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Ireland
| | - Matthew S. McCabe
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Ireland
| | - Jaewoo Kim
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ken Lemon
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Michael McMenamy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland
| | - Catherine Duffy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland
| | - S. Louise Cosby
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland
| | - Sinéad M. Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Ireland
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Cai Y, Ma F, Qu L, Liu B, Xiong H, Ma Y, Li S, Hao H. Weighted Gene Co-expression Network Analysis of Key Biomarkers Associated With Bronchopulmonary Dysplasia. Front Genet 2020; 11:539292. [PMID: 33033495 PMCID: PMC7509191 DOI: 10.3389/fgene.2020.539292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 08/18/2020] [Indexed: 12/05/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a complex disorder resulting from interactions between genes and the environment. The accurate molecular etiology of BPD remains largely unclear. This study aimed to identify key BPD-associated genes and pathways functionally enriched using weighted gene co-expression network analysis (WGCNA). We analyzed microarray data of 62 pre-term patients with BPD and 38 pre-term patients without BPD from Gene Expression Omnibus (GEO). WGCNA was used to construct a gene expression network, and genes were classified into definite modules. In addition, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of BPD-related hub genes were performed. Firstly, we constructed a weighted gene co-expression network, and genes were divided into 10 modules. Among the modules, the yellow module was related to BPD progression and severity and included the following hub genes: MMP25, MMP9, SIRPA, CKAP4, SLCO4C1, and SLC2A3; and the red module included some co-expression molecules that displayed a continuous decline in expression with BPD progression and included the following hub genes: LEF1, ITK, CD6, RASGRP1, IL7R, SKAP1, CD3E, and ICOS. GO and KEGG analyses showed that high expression of inflammatory response-related genes and low expression of T cell receptor activation-related genes are significantly correlated with BPD progression. The present WGCNA-based study thus provides an overall perspective of BPD and lays the foundation for identifying potential pathways and hub genes that contribute to the development of BPD.
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Affiliation(s)
- Yao Cai
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Fei Ma
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - LiuHong Qu
- Department of Neonatology, The Maternal and Child Health Care Hospital of Huadu, Guangzhou, China.,Huadu Affiliated Hospital of Guangdong Medical University, Guangzhou, China
| | - Binqing Liu
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hui Xiong
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanmei Ma
- Laboratory of Inborn Metabolism Errors, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sitao Li
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hu Hao
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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7
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Besteman SB, Callaghan A, Langedijk AC, Hennus MP, Meyaard L, Mokry M, Bont LJ, Calis JJA. Transcriptome of airway neutrophils reveals an interferon response in life-threatening respiratory syncytial virus infection. Clin Immunol 2020; 220:108593. [PMID: 32920212 DOI: 10.1016/j.clim.2020.108593] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND Neutrophils are the most abundant cell type infiltrating the airways during severe respiratory syncytial virus (RSV) infection. Their exact role in disease pathophysiology remains enigmatic. Therefore, we determined genome-wide RNA expression profiles of local and systemic neutrophils in RSV bronchiolitis to provide further insight into local neutrophil biology. METHODS We performed a single-center analysis, in 16 infants, admitted to the pediatric intensive care unit with severe RSV bronchiolitis. Neutrophils were isolated from blood and tracheobronchial aspirates (sputum). After low input RNA sequencing, differential expression of genes was determined followed by gene set analysis. RESULTS Paired transcriptomic analysis of airway versus blood neutrophils showed an inflammatory phenotype, characterized by NF-kB signaling and upregulated expression of IL-6 and interferon pathways. We observed distinct expression of neutrophil activation genes (TNFSF13B, FCER1G). DISCUSSION Our data indicate that airway neutrophils regulate their function at the transcriptional level in response to viral infection. It also suggests that local interferon drives the neutrophil response of severe RSV bronchiolitis.
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Affiliation(s)
- Sjanna B Besteman
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Amie Callaghan
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Annefleur C Langedijk
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Marije P Hennus
- Department of Paediatric Intensive Care, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Linde Meyaard
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Oncode Institute, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Michal Mokry
- Department of cardiology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Louis J Bont
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Jorg J A Calis
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Department of cardiology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
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8
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Vieira SE, Bando SY, Lauterbach GDP, Moreira-Filho CA. Human Leukocyte Transcriptional Response to SARS-CoV-2 Infection. Clinics (Sao Paulo) 2020; 75:e2078. [PMID: 32578831 PMCID: PMC7297521 DOI: 10.6061/clinics/2020/e2078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sandra Elisabete Vieira
- Departamento de Pediatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Silvia Yumi Bando
- Departamento de Pediatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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Neves KC, Vieira SE. Conditions of vulnerability to the inadequate treatment of bronchiolitis. Rev Assoc Med Bras (1992) 2020; 66:187-193. [DOI: 10.1590/1806-9282.66.2.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/29/2019] [Indexed: 11/22/2022] Open
Abstract
SUMMARY OBJECTIVE To analyze clinical and demographic variables possibly associated with the prescriptions of non-recommended but routinely used therapies for infants with acute viral bronchiolitis. METHODS A cross-sectional study included hospitalized infants with bronchiolitis caused by the respiratory syncytial virus. Those with other associated infections and/or morbidities were excluded. The data were collected from medical records. RESULTS Among 120 cases, 90% used inhaled beta-agonists, 72.5% corticosteroids, 40% antibiotics, and 66.7% inhaled hypertonic saline solution. The use of bronchodilators did not present an independent association with another variable. More frequent use of corticosteroids was associated with low oximetry, longer hospitalization time, and age>3 months. Antibiotic therapy was associated with the presence of fever, longer hospitalization, and age>3 months. Inhaled hypertonic saline solution was associated with longer hospitalization time. CONCLUSIONS Non-recommended prescriptions were frequent. Corticosteroid and antibiotic therapy were associated with signs of severity, as expected, but interestingly, they were more frequently used in infants above 3m, which suggested less safety in the diagnosis of viral bronchiolitis in these patients. The use of bronchodilators was even more worrying since they were indiscriminately used, without association with another variable related to the severity or characteristics of the host. The use of the inhaled hypertonic solution, although not associated with severity, seems to have implied a longer hospitalization time. The identification of these conditions of greater vulnerability to the prescription of inappropriate therapies contributes to the implantation of protocols for the bronchiolitis treatment, for continuing education and for analysis of the effectiveness of the strategies employed.
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Affiliation(s)
- Kattia Cristina Neves
- Universidade de São Paulo, Brasil; Hospital do Servidor Público Estadual de São Paulo, Brasil
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Bougarn S, Boughorbel S, Chaussabel D, Marr N. A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. F1000Res 2019; 8:284. [PMID: 31231515 PMCID: PMC6567289 DOI: 10.12688/f1000research.18533.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
The human immune defense mechanisms and factors associated with good versus poor health outcomes following viral respiratory tract infections (VRTI), as well as correlates of protection following vaccination against respiratory viruses, remain incompletely understood. To shed further light into these mechanisms, a number of systems-scale studies have been conducted to measure transcriptional changes in blood leukocytes of either naturally or experimentally infected individuals, or in individual’s post-vaccination. Here we are making available a public repository, for research investigators for interpretation, a collection of transcriptome datasets obtained from human whole blood and peripheral blood mononuclear cells (PBMC) to investigate the transcriptional responses following viral respiratory tract infection or vaccination against respiratory viruses. In total, Thirty one31 datasets, associated to viral respiratory tract infections and their related vaccination studies, were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application designed for interactive query and visualization of integrated large-scale data. Quality control checks, using relevant biological markers, were performed. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation. Via this interface, users can generate web links to customized graphical views, which may be subsequently inserted into manuscripts to report novel findings. The GXB tool enables browsing of a single gene across projects, providing new perspectives on the role of a given molecule across biological systems in the diagnostic and prognostic following VRTI but also in identifying new correlates of protection. This dataset collection is available at:
http://vri1.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
- Salim Bougarn
- Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Sabri Boughorbel
- Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Damien Chaussabel
- Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Nico Marr
- Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
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