Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Fish Shellfish Immunol. 2011 Nov;31(5):716-24. doi: 10.1016/j.fsi.2010.08.022. Epub 2010 Sep 8.
Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. We obtained 10 million sequence reads from control and Salmonella-infected zebrafish embryos using a tag-based sequencing method (DGE or Tag-Seq) and 15 million reads using whole transcript sequencing (RNA-Seq), which respectively mapped to circa 65% and 85% of 28,716 known Ensembl transcripts. Both sequencing methods showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A lower overlap of 165 transcripts was observed with previous microarray data. Based on the combined sequencing-based and microarray-based transcriptome data we compiled an annotated reference set of infection-responsive genes in zebrafish embryos, encoding transcription factors, signal transduction proteins, cytokines and chemokines, complement factors, proteins involved in apoptosis and proteolysis, proteins with anti-microbial activities, as well as many known or novel proteins not previously linked to the immune response. Furthermore, by comparison of the deep sequencing data of S. typhimurium infection in zebrafish embryos with previous deep sequencing data of Mycobacterium marinum infection in adult zebrafish we derived a common set of infection-responsive genes. This gene set consists of known and putative innate host defense genes that are expressed both in the absence and presence of a fully developed adaptive immune system and that provide a valuable reference for future studies of host-pathogen interactions using zebrafish infection models.
肠炎沙门氏菌血清型 Typhimurium（S. typhimurium）细菌在斑马鱼胚胎中引起炎症和致死性感染。为了在转录组水平上描述胚胎先天宿主反应，我们通过 Illumina 下一代测序分析扩展和验证了之前的微阵列数据。我们使用基于标签的测序方法（DGE 或 Tag-Seq）从对照和沙门氏菌感染的斑马鱼胚胎中获得了 1000 万个序列读数，使用全转录组测序（RNA-Seq）获得了 1500 万个读数，分别映射到 28716 个已知 Ensembl 转录物的大约 65%和 85%。两种测序方法均显示出转录物序列读数计数之间的强相关性，并且有 241 个转录物对感染有差异表达。与之前的微阵列数据相比，观察到较低的重叠度为 165 个转录物。基于组合的基于测序和基于微阵列的转录组数据，我们编译了斑马鱼胚胎中感染反应基因的注释参考集，这些基因编码转录因子、信号转导蛋白、细胞因子和趋化因子、补体因子、参与细胞凋亡和蛋白水解的蛋白质、具有抗菌活性的蛋白质，以及许多以前与免疫反应无关的已知或新蛋白质。此外，通过比较肠炎沙门氏菌感染在斑马鱼胚胎中的深度测序数据与之前在成年斑马鱼中分枝杆菌感染的深度测序数据，我们得出了一个共同的感染反应基因集。这个基因集由已知和推定的先天宿主防御基因组成，这些基因在没有和存在完全发育的适应性免疫系统的情况下都有表达，为使用斑马鱼感染模型研究宿主-病原体相互作用提供了有价值的参考。
