College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
Department of Food Toxicology and Contaminants, National Research Centre, Dokki, Cairo, 12622, Egypt.
BMC Genomics. 2022 Aug 13;23(1):587. doi: 10.1186/s12864-022-08808-x.
The cardiovascular developmental process is a tightly regulated network involving multiple genes. The current understanding of the molecular mechanism behind cardiovascular development is insufficient and requires further research.
Transcriptome sequencing of three developmental stages in zebrafish embryos was performed and revealed three key cardiovascular developmental stages. Then, the differentially expressed genes (DEGs) involved in cardiovascular development were screened out. The three developmental stages were 18 (T1), 24 (T2), and 42 h post fertilization (hpf) (T3), and the three stages were confirmed by detecting differences in expression between cardiomyocyte and endothelial marker genes (cmlc2, fli1) using in situ hybridization, which represents the characteristics of cardiovascular development. Thousands of DEGs were identified using transcriptome analysis. Of them, 2605 DEGs were in T1-vs-T2, including 2003 up-regulated and 602 down-regulated genes, 6446 DEGs were in T1-vs-T3, consisting of 4608 up-regulated and 1838 down-regulated genes, and 3275 DEGs were in T2-vs-T3, including 2420 up-regulated and 855 down-regulated genes. There were 644 common DEGs and 167 common five-fold higher differentially expressed genes (HDEGs) identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Significant differences was observed in the levels of gene expression among different developmental stages in multiple GO terms and KEGG pathways, such as cell migration to the midline involved in heart development, cardiovascular system development, circulatory system process for biological processes of GO terms; and cardiac muscle contraction, adrenergic signaling in cardiomyocytes for KEGG pathways. These results demonstrated that these three stages were important period for the development of the cardiovascular system. Lastly, we used quantitative real-time PCR (qPCR) to validate the reliability of RNA-sequencing by selecting 21 DEGs.
These results demonstrated that these three stages represented the important periods for cardiovascular system development of zebrafish and some candidate genes was obtained and provided a solid foundation for additional functional studies of the DEGs.
心血管发育过程是一个受多个基因调控的紧密网络。目前对心血管发育背后的分子机制的了解还不够充分，需要进一步研究。
对斑马鱼胚胎三个发育阶段进行转录组测序，揭示了三个关键的心血管发育阶段。然后，筛选出与心血管发育相关的差异表达基因（DEGs）。这三个发育阶段分别为受精后 18（T1）、24（T2）和 42 小时（T3），通过原位杂交检测心肌细胞和内皮标记基因（cmlc2、fli1）之间的表达差异来确认这三个阶段，这代表了心血管发育的特征。通过转录组分析鉴定了数千个 DEGs。其中，T1 与 T2 相比有 2605 个 DEGs，包括 2003 个上调和 602 个下调基因，T1 与 T3 相比有 6446 个 DEGs，包括 4608 个上调和 1838 个下调基因，T2 与 T3 相比有 3275 个 DEGs，包括 2420 个上调和 855 个下调基因。鉴定出 644 个共同 DEGs 和 167 个共同五倍差异表达基因（HDEGs），并使用数据库 for Annotation, Visualization and Integrated Discovery (DAVID) 对其进行基因本体论 (GO) 和京都基因与基因组百科全书 (KEGG) 通路富集分析。GO 术语和 KEGG 通路中的多个生物学过程，如涉及心脏发育、心血管系统发育、循环系统过程的细胞迁移到中线；以及 KEGG 通路中的心肌收缩、心肌细胞中的肾上腺素能信号传导，都观察到不同发育阶段之间基因表达水平存在显著差异。这些结果表明，这三个阶段是心血管系统发育的重要时期。最后，我们通过选择 21 个 DEGs 进行定量实时 PCR (qPCR) 验证了 RNA-seq 的可靠性。
这些结果表明，这三个阶段代表了斑马鱼心血管系统发育的重要时期，并获得了一些候选基因，为 DEGs 的进一步功能研究提供了坚实的基础。
