Abstract Understanding how a zygote develops from a single cell into a multicellular organism has benefitted from single-cell tools, including RNA sequencing (RNA-Seq) and immunofluorescence (IF). However, scrutinizing inter- and intra-embryonic phenotypic variation is hindered by two fundamental limitations; the loose correlation between transcription and translation and the cross-reactivity of immunoreagents. To address these challenges, we describe a high-specificity microfluidic immunoblot optimized to quantify protein expression from all stages of mouse preimplantation development. Despite limited availability of isoform-specific immunoreagents, the immunoblot resolves inter-embryonic heterogeneity of embryo-specific isoforms (i.e., DICER-1). We observed significantly higher DICER-1 isoform expression in oocytes when compared to two-cell embryos, and further find that protein expression levels follow the same trend as mRNA for both the full-length and truncated DICER-1 isoforms. At the morula stage, we assayed both whole and disaggregated embryos for loading controls (β-tubulin, GAPDH) and markers that regulate cell fate decisions (CDX-2, SOX-2). In disaggregated morula, we found that cell volume showed positive, linear correlation with expression of β-tubulin and SOX-2. In dissociated two-cell and four-cell blastomeres, we detect significant inter-blastomeric variation in GADD45a expression, corroborating suspected cellular heterogeneity even in the earliest multicellular stage of preimplantation embryos. As RNA-Seq and other transcript-centric approaches continue to further probe preimplantation development, the demand for companion protein-based techniques rises. The reported microfluidic immunoblot serves as an essential tool for understanding mammalian development by providing high-specificity and direct measurements of protein targets at single-embryo and single-blastomere resolution.

Single-embryo and single-blastomere immunoblotting reports protein expression heterogeneity in early-stage preimplantation embryos