Multi-stage transcriptomic analysis of mouse embryonic lethality induced by homozygous knockout of the Vrtn gene

The Vrtn gene, a recently identified regulator of embryonic development and stem cell pluripotency, is essential for embryonic survival, as its homozygous knockout (Vrtn^-/-) leads to lethality in mice at approximately embryonic day 12.5 (E12.5). To elucidate the underlying lethal mechanism, an integrated approach combining morphological observation, multi-stage transcriptomic analysis, and functional validation experiments was employed to systematically investigate the developmental disorders caused by Vrtn deficiency. Morphological observation showed that Vrtn^-/^- embryos exhibited significant abnormalities at developmental stages E9.0, E9.5, E10.0, E10.5, and E11.0, including shortened body axis, defective neural tube closure, aberrant somite differentiation, and cardiovascular malformations, accompanied by overall developmental delay. At the molecular level, through RNA sequencing and qRT-PCR validation revealed that Vrtn deficiency not only suppressed the expression of genes critical for somitogenesis (Hoxa2, Hes5), neurodevelopment (Nefm, Nefl), and the hematopoietic system (Hbb-bh1, Klf1), but also aberrantly activated genes associated with apoptosis (Crabp2, Fam162a) and lipid metabolism (Apom, Apoe). TUNEL staining showed that the level of apoptosis was significantly increased in Vrtn^-/- embryos. Meanwhile, immunofluorescence detection of Hif-1α indicated that the hypoxic stress response was aberrantly activated. Furthermore, the widespread dysregulation of genes involved in thyroid hormone transport (Ttr), DNA damage stress (Ddit4), and lipid metabolism (Apoa4, Apoa1) collectively exacerbated the developmental imbalance, ultimately leading to embryonic death. A cross-species analysis demonstrated that VRTN knockdown in human embryonic stem cells (hESCs) significantly suppressed the expression of core angiogenic genes (VEGFA, COL1A1 and HES1), a finding consistent with public database analyses indicating a strong association between VRTN and the hypoxic response. In conclusion, this study elucidates that Vrtn functions as a regulatory gene that maintains embryonic homeostasis by orchestrating multiple key developmental processes, including somitogenesis, neural differentiation, angiogenesis, and the hypoxic stress response. This discovery not only deepens the understanding of the role of Vrtn in embryonic development but also provides a new perspective for deciphering the pathogenesis of related hereditary diseases.