Tombácz Dóra, Maróti Zoltán, Oláh Péter, Dörmő Ákos, Gulyás Gábor, Kalmár Tibor, Csabai Zsolt, Boldogkői Zsolt
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, Szeged, 6720, Hungary.
MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Somogyi u. 4, Szeged, 6720, Hungary.
Sci Rep. 2025 Jan 25;15(1):3247. doi: 10.1038/s41598-025-87536-0.
In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants.
在我们的研究中，我们利用基于纳米孔MinION技术的直接cDNA测序，对感染马疱疹病毒1型（EHV-1）的宿主细胞进行了时间转录组分析。测序读数用于在各个时间点进行转录本定量。通过edgeR软件包鉴定病毒感染诱导的差异基因表达。根据其动力学特征将鉴定出的基因分为六组。最初的三个簇包含立即早期反应基因，通常是转录因子和抗病毒信号通路的元件。这些基因在早期感染阶段要么上调（簇1），要么下调（簇2和簇3）。其余三个簇包括晚期反应基因。在这些类别中，很难确定基因表达的变化是直接与病毒感染相关，还是仅仅是感染的副作用。使用STRINGDB软件进行的基因关联研究揭示了几个可能直接受病毒影响的基因网络。我们还使用基因调控网络数据库探讨了基因共表达是否可能是上游转录因子对它们进行集体调控的结果。最后，我们的差异转录本使用（DTU）分析确定了一些与未感染细胞相比，转录本异构体比例发生改变的基因。因此，我们的分析表明，EHV-1感染不仅会改变宿主基因表达，还会导致转录本异构体的差异使用，特别是剪接变体。
