Publicação
Deciphering the importance of peroxisomes in the context of viral infections through transcriptomic analyses
| Resumo: | Peroxisomes are multifunctional organelles central to lipid metabolism, redox homeostasis, and innate immunity. Increasing evidence highlights their dynamic involvement in viral infections, where viruses remodel peroxisomal abundance, distribution, and function to facilitate replication while evading host antiviral defenses. Despite substantial experimental work on peroxisome-virus interactions, a systematic bioinformatic exploration of peroxisomal gene regulation across distinct viral infections remains largely unexplored. Viral infections remain a major health challenge, with mutations often undermining the efficacy of virus-specific treatments. Hence, there is a growing interest in identifying host cell mechanisms as targets for the development of novel antivirals. Peroxisomal mechanisms are promising candidates, as these organelles have been pinpointed as key players during viral infections. However, detailed knowledge on the underlying mechanisms is still scarce. In this study, we performed a transcriptomic analysis of peroxisomal genes at several stages of infection by influenza A virus (IAV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), and several flaviviruses, such as, dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), yellow fever virus (YFV), and tick-borne encephalitis virus (TBEV), from human cell line-infected samples. Raw RNA-seq datasets (compressed FASTQ format) were retrieved from publicly available repositories and processed through a standard pipeline, involving STAR and StringTie, to obtain gene-level read counts, which were then analyzed with the DESeq2 R package. Exploratory data analysis was performed to evaluate sample variability and condition-specific clustering, followed by differential expression analysis across the different infection stages. Our findings show transcriptional changes between infected and non-infected samples, with significant up- or downregulation in genes encoding peroxisomal proteins. These variations, particularly affecting genes involved in lipid metabolism, were more pronounced at specific infection stages. These results provide key insights for identifying peroxisome-related targets against IAV, flaviviruses, and SARS-CoV-2. Subsequently, complementary functional studies were performed using BEAS-2B cells infected with HCoV-229E, which demonstrated that ACBD5 gene silencing does not affect viral protein transcription, as verified by viral nucleoprotein (NP) accumulation, and decreases immune response. However, despite this condition favorable to viral replication, there is no increase in the infectivity of the virions produced. These results suggest that the ACBD5 protein contributes both to antiviral signaling and to lipid remodeling, which is essential for the formation of new virions, since disruption of the physical-functional interaction between peroxisomes and the endoplasmic reticulum compromises lipid exchange, potentially altering the membrane composition essential for the formation of coronavirus replication organelles and virion maturation. Thus, this work, through the exploration of ACBD5 silencing and the presentation of peroxisomal gene regulation patterns in the context of infection, seeks to point to new host-focused therapeutic targets to be explored. |
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| Autores principais: | Almeida, Francisco Rodrigues |
| Assunto: | Peroxisomes Viral infections Bioinformatics Transcriptomics Peroxisomal metabolism Human coronavirus 229E SARS-CoV-2 Influenza A virus Flaviviruses |
| Ano: | 2025 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso embargado |
| Instituição associada: | Universidade de Aveiro |
| Idioma: | inglês |
| Origem: | RIA - Repositório Institucional da Universidade de Aveiro |
| Resumo: | Peroxisomes are multifunctional organelles central to lipid metabolism, redox homeostasis, and innate immunity. Increasing evidence highlights their dynamic involvement in viral infections, where viruses remodel peroxisomal abundance, distribution, and function to facilitate replication while evading host antiviral defenses. Despite substantial experimental work on peroxisome-virus interactions, a systematic bioinformatic exploration of peroxisomal gene regulation across distinct viral infections remains largely unexplored. Viral infections remain a major health challenge, with mutations often undermining the efficacy of virus-specific treatments. Hence, there is a growing interest in identifying host cell mechanisms as targets for the development of novel antivirals. Peroxisomal mechanisms are promising candidates, as these organelles have been pinpointed as key players during viral infections. However, detailed knowledge on the underlying mechanisms is still scarce. In this study, we performed a transcriptomic analysis of peroxisomal genes at several stages of infection by influenza A virus (IAV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), and several flaviviruses, such as, dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), yellow fever virus (YFV), and tick-borne encephalitis virus (TBEV), from human cell line-infected samples. Raw RNA-seq datasets (compressed FASTQ format) were retrieved from publicly available repositories and processed through a standard pipeline, involving STAR and StringTie, to obtain gene-level read counts, which were then analyzed with the DESeq2 R package. Exploratory data analysis was performed to evaluate sample variability and condition-specific clustering, followed by differential expression analysis across the different infection stages. Our findings show transcriptional changes between infected and non-infected samples, with significant up- or downregulation in genes encoding peroxisomal proteins. These variations, particularly affecting genes involved in lipid metabolism, were more pronounced at specific infection stages. These results provide key insights for identifying peroxisome-related targets against IAV, flaviviruses, and SARS-CoV-2. Subsequently, complementary functional studies were performed using BEAS-2B cells infected with HCoV-229E, which demonstrated that ACBD5 gene silencing does not affect viral protein transcription, as verified by viral nucleoprotein (NP) accumulation, and decreases immune response. However, despite this condition favorable to viral replication, there is no increase in the infectivity of the virions produced. These results suggest that the ACBD5 protein contributes both to antiviral signaling and to lipid remodeling, which is essential for the formation of new virions, since disruption of the physical-functional interaction between peroxisomes and the endoplasmic reticulum compromises lipid exchange, potentially altering the membrane composition essential for the formation of coronavirus replication organelles and virion maturation. Thus, this work, through the exploration of ACBD5 silencing and the presentation of peroxisomal gene regulation patterns in the context of infection, seeks to point to new host-focused therapeutic targets to be explored. |
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