Comparative proteomic landscapes elucidate human preimplantation development and failure

Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility. For gene knock out, mouse zygotes were collected by superovulation of 3- to 4-week-old B6D2F1 females mated with males of the same strain. Cas9 protein (final concentration 100 ng/μL) was mixed with three different sgRNAs (final concentration 50 ng/μL per sgRNA) and injected into the cytoplasm of zygotes in M2 medium with CB using a Piezo-driven micromanipulator (Prime Tech). Then, the injected embryos were cultured in KSOM medium at 37 °C with 5% CO2.