Dissecting human embryonic patterning during organogenesis reveals a rostral midline progenitor population for mesoendoderm induction

Abstract

Understanding how human organogenesis is accomplished via intricate spatiotemporal patterning of organ primordia requires spatial atlases at cellular resolution. However, existing human embryo spatial atlases are built using sequencing-based platforms such as Stereo-seq, which have limited spatial resolution and blurred anatomical boundaries, leading to misclassification across adjacent cells. Here, we integrate in situ imaging-based transcriptomics (Xenium) with transcriptome-wide spatial profiling (Visium-HD) of Carnegie stages 9-12 embryos to delineate the patterning of core embryonic tissues at single-cell resolution, including the brain, spinal cord, somites, neural crest, notochord, heart, and gut tube. A new finding enabled by spatial single-cell resolution is the identification of rostral midline progenitors (RMPs), a cell population co-expressing SOX2, TBXT, and OTX2. Transcriptionally, RMPs are distinct from both neuromesodermal progenitors (NMPs) and prechordal mesoderm, and in vivo clonal barcoding in mice indicates that RMPs share a common developmental origin with rostral neural ectoderm. To interrogate their functional significance, we leveraged our spatial transcriptome data to recapitulate RMP-like cells from human pluripotent stem cells and showed that these cells can induce epiblast-like cells to acquire mesendodermal and endodermal fates, while themselves adopting an ectodermal fate consistent with their in vivo counterparts. This work provides a 3D, stage-resolved molecular cell atlas of tissue patterning in human embryo that serves as a reference for in vitro models.