Decoding Embryonic Fates: Lineages, Mechanisms, and Spatial Context

Genetic lineage tracing and signaling recorders have transformed our view of fate decisions, but flexible application in mouse embryos is limited by poor access and delivery. We developed NEPTUNE (Neural Plate Targeting by in Utero Nano-injection), lentiviral nano-injection at E7.5 that targets up to 99% of neural progenitors. Introducing barcoded libraries with NEPTUNE enabled comprehensive lineage tracing of the nervous system at E9.5–E10.5 and postnatal cochlea, revealing early anterior–posterior compartmentalization and detailed cochlear lineage relationships.
In ongoing work, we have extended in utero barcode delivery to target other cell types. Combining this with high-resolution single-cell readouts, and VisiumHD on matched organs/time points, we are deconvolving cell types and uncovering spatial developmental programs. These datasets yield comprehensive lineage maps and clarify trajectories in organ systems previously difficult to manipulate in utero.
Together, NEPTUNE and in utero barcoding provide a versatile, scalable platform for precise, high-coverage targeting and multi-modal lineage reconstruction in vivo, enabling mechanistic insights into mammalian organogenesis that were previously inaccessible.