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Master's Dissertation
DOI
https://doi.org/10.11606/D.42.2022.tde-31052022-085711
Document
Author
Full name
Ivana Silva Ferreira
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2022
Supervisor
Committee
Marques, Otávio Cabral (President)
Câmara, Niels Olsen Saraiva
Carvalho, Robson Francisco
Miranda, Gustavo Cabral de
Title in Portuguese
O interactoma de RNA mensageiros e microRNAs em cardiomiócitos infectados com SARS-CoV-2
Keywords in Portuguese
cardiomiócitos infectados
microRNA
SARS-CoV-2
Abstract in Portuguese
A atual doença COVID-19 (do inglês, coronavirus disease 2019) tornou-se rapidamente uma pandemia, configurando um estado de emergência pública internacional. O vírus causador da doença, denominado síndrome respiratória aguda grave coronavírus 2 (SARS-CoV-2) desencadeia manifestações clínicas que variam de casos assintomáticos à síndrome respiratória aguda grave e à morte. Além dos sintomas respiratórios, pacientes com COVID-19 podem apresentar complicações cardíacas, incluindo miocardite viral e arritmias. Embora as respostas isquêmicas e inflamatórias causadas por COVID-19 possam afetar negativamente a função cardíaca, o impacto direto da infecção em cardiomiócitos humanos ainda não é bem compreendido. Muitos pesquisadores estão explorando as alterações moleculares a nível transcricional, porém pouco se sabe sobre os fatores que regulam pós-transcricionalmente a expressão gênica após a infecção. Os microRNAs (miRs) são uma classe de pequenos RNAs não codificantes que regulam pós- transcricionalmente a expressão gênica e apresentam um potencial terapêutico em diversas patologias. Buscamos identificar nesse estudo o perfil específico de expressão de miRs e vias moleculares envolvidas na resposta imune ao SARS-CoV-2 em cardiomiócitos . Realizamos uma abordagem de imunologia sistêmica e integrativa de dados transcriptômicos, objetivando à identificação das redes moleculares reguladas por miRs. Utilizamos a ferramenta NetworkAnalyst 3.0 para a análise de expressão diferencial de dados de RNA sequencing (RNAseq) de quatro conjuntos de dados de transcriptoma de cardiomiocitos infectados com SARS-CoV-2. Os read counts foram utilizados para identificação dos genes diferencialmente expressos (DEGs) através do pipeline DESeq2. Os processos biológicos enriquecidos foram identificados através das ferramentas WebGestalt e EnrichR. Enquanto DEGs up-regulados em todos esses estudos enriqueceram processos biológicos relacionados à resposta imune (ex: ativação de células T, produção de citocinas e regulação da hematopoiese), os down-regulados enriqueceram genes relacionados a desregulação do metabolismo (ex: montagem do complexo NADPH desidrogenase; geração de metabólitos precursores e energia; processo catabólico de pequena molécula) e do sistema muscular. Foram identificados um total de 601 DEGs comuns entre todos os conjuntos de dados. Para a análise do interactoma dos mRis e desses mRNA, focamos em DEGs associados à resposta imune, contração do músculo cardíaco, remodelação da matriz extracelular e coagulação. Utilizando a ferramenta MiRTarBase, identificamos 331 potenciais miRs reguladores dos DEGs de cardiomiócitos infectados. Destes, 19 miRs são potenciais reguladores de genes de resposta imune, 4 miRs associados à contração do músculo cardíaco, 21 associados a matriz extracelular e 6 reguladores de alvos associados à coagulacão. Destacamos alguns miRs que potencialmente regulam os genes envolvidos na resposta inflamatória e via de sinalização de interferon do tipo I, como miR-155-5p e os envolvidos com o processo de contração da célula muscular cardíaca como miR-29a-3p, miR-29b- 3p e miR-146b-3p. Nossa análise sistêmica e integrativa de miRs-mRNA identificou possíveis redes e vias moleculares reguladoras, revelando potenciais miRs e genes relacionados a resposta imune em cardiomiócitos infectados com SARS-CoV-2. Na última etapa desse projeto realizaremos uma abordagem experimental para avaliarmos a expressão desses miRs e proteínas expressas pelos cardiomiócitos através da análise do microRNAoma e do proteoma das células infectados com o SARS-CoV-2.
Title in English
The interactome of messenger RNA and microRNAs in cardiomyocytes infected with SARS-Cov-2
Keywords in English
infected cardiomyocytes
microRNA
SARS-CoV-2
Abstract in English
The Coronavirus 2019 (COVID-19) quickly became a pandemic, configuring an international public state of emergency. The virus that causes the disease, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers clinical manifestations ranging from asymptomatic infection to severe acute respiratory syndrome and death. In addition to respiratory symptoms, patients with COVID-19 may experience cardiac complications, including viral myocarditis and arrhythmias. Although the ischemic and inflammatory responses caused by COVID-19 can negatively affect cardiac function, the direct impact of the infection on human cardiomyocytes is still not well understood. Many researchers are exploring molecular changes at the transcriptional level, but little is known about the factors that post-transcriptionally regulate gene expression during SARS-CoV-2 infection. MicroRNAs (miRs) are a class of small non- coding RNAs that post-transcriptionally regulate gene expression and have therapeutic potential in several pathologies. We employed a systems and integrative immunology approach by analyzing transcriptomic data, aiming to identify the molecular networks regulated by miRs. We used the NetworkAnalyst 3.0 tool for differential expression analysis of RNA sequencing (RNAseq) data from four public datasets. Read counts were used to identify differentially expressed genes (DEGs) through the DESeq2 pipeline. The enriched biological processes identified using the WebGestalt and EnrichR tools. While up-regulated DEGs across these studies enriched BPs related to the immune response (e.g., T cell activation, cytokine production and regulation of hematopoiesis), the down-regulated DEGs enriched BPs related to metabolic dysregulation (e.g., complex assembly NADPH dehydrogenase; generation of precursor metabolites and energy; small molecule catabolic process) and the muscular system. A total of 601 common DEGs across all datasets were identified. For the interactome analysis of mRis and these common DEGs, we focused on those associated with the immune response, cardiac muscle contraction, extracellular matrix remodeling and thrombosis, using the QUICKgo platform to select BPs while avoiding overlapping category terms Using the MiRTarBase tool, we identified 331 potential regulatory miRs of SARS-CoV-2 infected cardiomyocytes Of these, 19 miRs are potential regulators of immune response genes, 4 miRs associated with cardiac muscle contraction, 21 associated with extracellular matrix and 6 target regulators associated with coagulation. Of note, there are miRs that potentially regulate genes involved in the inflammatory response and interferon type I signaling pathway, such as miR-155-5p and those involved in the cardiac muscle cell contraction process, such as miR-29a-3p, miR-29b -3p and miR-146b-3p. Our systems and integrative immunology approach of identified possible miRs- mRNA regulatory molecular networks and pathways potentially associated with immune response-related molecules of cardiomyocytes infected with SARS-CoV-2. In the last phase of this project, we will carry out an experimental approach to evaluate the expression of these miRs and proteins by SARS-CoV-2 infected cardiomyocytes through the analysis of their microRNAoma and proteome.
 
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Release Date
2024-05-30
Publishing Date
2022-12-09
 
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