A Comparison between In Vivo and Whole Embryo Culture using Transcriptomics: Developmental Changes, Model Differences and Retinoic Acid Response

Cultured embryos mimic the morphological developmental progression of embryos (in vivo) undergoing neurulation and early organogenesis. Using available genomics technologies, comparative molecular-based assessments between cultured embryos and in vivo models may further clarify commonalities and dissimilarities which contribute to differences between systems. Therefore, in this study, using a transcriptomic approach, we compared cultured whole rat embryos and embryos in vivo at comparable time points in development (gestational day (GD) 10 + 2-48h, GD 0 = copulatory plug) to assess for commonalities and differences in gene expression in relation to morphology. We reveal strong parallels in time-dependent expression of genes in terms of magnitude, directionality and functionality between whole embryo culture (WEC) and in vivo (rat). Genes changing in expression over time resemble previously hypothesized mechanisms underlying early development in mammalian systems. Furthermore, at the gene and functional level, we identify genes which differ in expression between models, including genes related to development, oxygen transport and metabolism. In summary, our results support the use of WEC for toxicological studies aimed at representing in vivo development during this time-window at the molecular level. Additionally, we indicate genes which differ in expression between models, providing possible insights for improvement of culture conditions.体外培养胚胎能够模拟经历神经胚形成（neurulation）和早期器官发生（organogenesis）的体内（in vivo）胚胎的形态发育进程。借助现有基因组学技术，对体外培养胚胎与体内模型开展分子层面的比较分析，可进一步阐明两类系统间产生共性与差异的根本原因。因此，本研究采用转录组学（transcriptomic）方法，对发育时程匹配的体外培养全大鼠胚胎与体内胚胎（妊娠天数（gestational day, GD）10 + 2-48小时，GD0定义为观察到交配栓（copulatory plug）当日）进行比较，以评估与形态相关的基因表达共性与差异。本研究发现，全胚胎培养（Whole Embryo Culture, WEC）与大鼠体内模型之间，基因的时序表达在表达幅度、变化方向及功能层面均存在高度相似性。随时间推移表达量发生改变的基因，其特征与此前学界提出的哺乳动物早期发育潜在机制高度吻合。此外，本研究在基因与功能层面鉴定出两类模型间表达存在差异的基因，其中涵盖与发育、氧转运及代谢相关的基因。综上，本研究结果证实，全胚胎培养（WEC）可用于旨在从分子层面模拟该发育时程体内发育过程的毒理学研究。此外，本研究还鉴定出两类模型间表达存在差异的基因，为优化体外培养体系提供了潜在思路。