Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050001, Colombia.
Viruses. 2024 Jun 20;16(6):996. doi: 10.3390/v16060996.
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.
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.
We found that IL27, similar to IFNs, upregulates several TRIM genes' expression in human macrophages. Specifically, we identified three common TRIM genes (, , and ) induced by IL27 and all types of human IFNs. Additionally, we performed the first report of transcriptional regulation of , , , and 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.
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.
三基序（TRIM）家族包括 80 多种不同的人类基因。它们的功能与调节细胞内信号转导、转录、自噬和先天免疫等重要细胞过程有关。在病毒感染期间，巨噬细胞是先天免疫的关键组成部分，可产生干扰素（IFNs）和白细胞介素 27（IL27）。我们最近发表的研究表明，IL27 和 IFNs 诱导各种基因的转录变化，包括参与 JAK-STAT 信号转导的基因。此外，IL27 和 IFNs 在单核细胞来源的巨噬细胞（MDMs）中共享促炎和抗病毒途径，导致炎症因子和干扰素刺激基因（ISGs）的表达既有共同之处，也有独特之处，ISGs 编码抗病毒蛋白。有趣的是，近年来，许多 TRIM 蛋白已被认为是 ISGs。虽然已经非常清楚 TRIM 的表达是由 IFNs 诱导的，但尚不完全清楚 IL27 是否会在巨噬细胞中诱导 TRIM 基因的表达。因此，在这项研究中，我们研究了 IL27 和 I 型、II 型和 III 型 IFNs 刺激对 MDMs 中 TRIM 基因 mRNA 表达谱的影响。
我们使用批量 RNA-seq 来检查 IFNs 或 IL27 处理的 MDMs 中 TRIM 的表达谱。最初，我们使用热图来描述不同 TRIM 亚家族的表达模式。随后，使用火山图来识别常见差异表达的 TRIM 基因。此外，我们使用 ClueGO 进行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 对马亚罗病毒复制的影响。
我们发现，IL27 与 IFNs 类似，可上调人巨噬细胞中几种 TRIM 基因的表达。具体而言，我们鉴定出三个受 IL27 和所有类型人 IFNs 诱导的共同 TRIM 基因（、和）。此外，我们首次报告了 、 、 和 基因对 IL27 反应的转录调控。TRIM 涉及广泛的生物学过程，包括对病毒的防御反应、病毒生命周期的调节以及对病毒过程的负调节。此外，我们观察到先前用 IL27 处理的 MDMs 中马亚罗病毒复制减少。
我们的研究结果表明，IL27 与 IFNs 一样，调节参与先天免疫诱导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，与 IFN 一样，IL27 降低了 MDMs 中的马亚罗病毒复制。这意味着 IL27 和 IFNs 在功能水平上具有许多相似之处。此外，鉴定出对 IL27 反应的不同 TRIM 亚群及其差异表达为理解人类巨噬细胞中抗病毒反应的调控机制提供了新的见解。
