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Abstract：
BACKGROUND: The Tripartite motif (TRIM) family includes more than 80 distinct human genes. Their function has been implicated in regulating important cellular processes, including intracellular signaling, transcription, autophagy, and innate immunity. During viral infections, macrophages are key components of innate immunity that produce interferons (IFNs) and IL27. We recently published that IL27 and IFNs induce transcriptional changes in various genes, including those involved in JAK-STAT signaling. Furthermore, IL27 and IFNs share proinflammatory and antiviral pathways in monocyte-derived macrophages (MDMs), resulting in both common and unique expression of inflammatory factors and IFN-stimulated genes (ISGs) encoding antiviral proteins. Interestingly, many TRIM proteins have been recognized as ISGs in recent years. Although it is already very well described that TRIM expression is induced by IFNs, it is not fully understood whether TRIM genes are induced in macrophages by IL27. Therefore, in this study, we examined the effect of stimulation with IL27 and type I, II, and III IFNs on the mRNA expression profiles of TRIM genes in MDMs.
METHODS: We used bulk RNA-seq to examine the TRIM expression profile of MDMs treated with IFNs or IL27. Initially, we characterized the expression patterns of different TRIM subfamilies using a heatmap. Subsequently, a volcano plot was employed to identify commonly differentially expressed TRIM genes. Additionally, we conducted gene ontology analysis with ClueGO to explore the biological processes of the regulated TRIMs, created a gene-gene interaction network using GeneMANIA, and examined protein-protein interactions with the STRING database. Finally, RNA-seq data was validated using RT-qPCR. Furthermore, the effect of IL27 on Mayaro virus replication was also evaluated.
RESULTS: We found that IL27, similar to IFNs, upregulates several TRIM genes\' expression in human macrophages. Specifically, we identified three common TRIM genes (TRIM19, 21, and 22) induced by IL27 and all types of human IFNs. Additionally, we performed the first report of transcriptional regulation of TRIM19, 21, 22, and 69 genes in response to IL27. The TRIMs involved a broad range of biological processes, including defense response to viruses, viral life cycle regulation, and negative regulation of viral processes. In addition, we observed a decrease in Mayaro virus replication in MDMs previously treated with IL27.
CONCLUSIONS: Our results show that IL27, like IFNs, modulates the transcriptional expression of different TRIM-family members involved in the induction of innate immunity and an antiviral response. In addition, the functional analysis demonstrated that, like IFN, IL27 reduced Mayaro virus replication in MDMs. This implies that IL27 and IFNs share many similarities at a functional level. Moreover, identifying distinct TRIM groups and their differential expressions in response to IL27 provides new insights into the regulatory mechanisms underlying the antiviral response in human macrophages.
METHODS: We used bulk RNA-seq to examine the TRIM expression profile of MDMs treated with IFNs or IL27. Initially, we characterized the expression patterns of different TRIM subfamilies using a heatmap. Subsequently, a volcano plot was employed to identify commonly differentially expressed TRIM genes. Additionally, we conducted gene ontology analysis with ClueGO to explore the biological processes of the regulated TRIMs, created a gene-gene interaction network using GeneMANIA, and examined protein-protein interactions with the STRING database. Finally, RNA-seq data was validated using RT-qPCR. Furthermore, the effect of IL27 on Mayaro virus replication was also evaluated.
RESULTS: We found that IL27, similar to IFNs, upregulates several TRIM genes\' expression in human macrophages. Specifically, we identified three common TRIM genes (TRIM19, 21, and 22) induced by IL27 and all types of human IFNs. Additionally, we performed the first report of transcriptional regulation of TRIM19, 21, 22, and 69 genes in response to IL27. The TRIMs involved a broad range of biological processes, including defense response to viruses, viral life cycle regulation, and negative regulation of viral processes. In addition, we observed a decrease in Mayaro virus replication in MDMs previously treated with IL27.
CONCLUSIONS: Our results show that IL27, like IFNs, modulates the transcriptional expression of different TRIM-family members involved in the induction of innate immunity and an antiviral response. In addition, the functional analysis demonstrated that, like IFN, IL27 reduced Mayaro virus replication in MDMs. This implies that IL27 and IFNs share many similarities at a functional level. Moreover, identifying distinct TRIM groups and their differential expressions in response to IL27 provides new insights into the regulatory mechanisms underlying the antiviral response in human macrophages.
摘要：
背景：三方基序（TRIM）家族包括80多个不同的人类基因。它们的功能与调节重要的细胞过程有关，包括细胞内信号，转录,自噬,和先天免疫。在病毒感染期间，巨噬细胞是产生干扰素(IFN)和IL27的先天免疫的关键成分。我们最近发表了IL27和IFN诱导各种基因的转录变化，包括那些参与JAK-STAT信号。此外，IL27和IFN在单核细胞衍生的巨噬细胞（MDM）中共享促炎和抗病毒途径，导致炎症因子和编码抗病毒蛋白的IFN刺激基因（ISGs）的共同和独特表达。有趣的是,近年来许多TRIM蛋白被认为是ISGs。尽管已经很好地描述了TRIM表达是由IFN诱导的，目前尚不完全清楚TRIM基因是否在巨噬细胞中被IL27诱导。因此,在这项研究中，我们检查了IL27和I型刺激的效果，II,和IIIIFNs对MDMs中TRIM基因mRNA表达谱的影响。
方法：我们使用大量RNA-seq来检查用IFNs或IL27处理的MDMs的TRIM表达谱。最初，我们使用热图表征了不同TRIM亚家族的表达模式。随后，火山图用于鉴定常见差异表达的TRIM基因。此外,我们用ClueGO进行了基因本体论分析，以探索受调控的TRIMs的生物学过程，使用GeneMANIA创建了一个基因-基因相互作用网络，并使用STRING数据库检查蛋白质-蛋白质相互作用。最后,使用RT-qPCR验证RNA-seq数据。此外，还评估了IL27对Mayaro病毒复制的影响.
结果：我们发现IL27与IFNs相似，上调几种TRIM基因在人巨噬细胞中的表达。具体来说,我们确定了由IL27和所有类型的人IFN诱导的三种常见TRIM基因(TRIM19,21和22).此外,我们首次报道了TRIM19,21,22和69基因响应IL27的转录调控.TRIM涉及广泛的生物过程，包括对病毒的防御反应，病毒生命周期调节，和病毒过程的负调控。此外,我们观察到之前接受IL27治疗的MDM中Mayaro病毒复制减少.
结论：我们的结果表明，IL27与IFNs一样，调节参与诱导先天免疫和抗病毒反应的不同TRIM家族成员的转录表达。此外,功能分析表明，像IFN一样，IL27减少了Mayaro病毒在MDM中的复制。这意味着IL27和IFN在功能水平上具有许多相似性。此外，确定不同的TRIM组及其响应IL27的差异表达为人类巨噬细胞抗病毒反应的调节机制提供了新的见解。
方法：我们使用大量RNA-seq来检查用IFNs或IL27处理的MDMs的TRIM表达谱。最初，我们使用热图表征了不同TRIM亚家族的表达模式。随后，火山图用于鉴定常见差异表达的TRIM基因。此外,我们用ClueGO进行了基因本体论分析，以探索受调控的TRIMs的生物学过程，使用GeneMANIA创建了一个基因-基因相互作用网络，并使用STRING数据库检查蛋白质-蛋白质相互作用。最后,使用RT-qPCR验证RNA-seq数据。此外，还评估了IL27对Mayaro病毒复制的影响.
结果：我们发现IL27与IFNs相似，上调几种TRIM基因在人巨噬细胞中的表达。具体来说,我们确定了由IL27和所有类型的人IFN诱导的三种常见TRIM基因(TRIM19,21和22).此外,我们首次报道了TRIM19,21,22和69基因响应IL27的转录调控.TRIM涉及广泛的生物过程，包括对病毒的防御反应，病毒生命周期调节，和病毒过程的负调控。此外,我们观察到之前接受IL27治疗的MDM中Mayaro病毒复制减少.
结论：我们的结果表明，IL27与IFNs一样，调节参与诱导先天免疫和抗病毒反应的不同TRIM家族成员的转录表达。此外,功能分析表明，像IFN一样，IL27减少了Mayaro病毒在MDM中的复制。这意味着IL27和IFN在功能水平上具有许多相似性。此外，确定不同的TRIM组及其响应IL27的差异表达为人类巨噬细胞抗病毒反应的调节机制提供了新的见解。
