Tracing developmental signaling histories with imaging-based molecular recording
openNIGMS - National Institute of General Medical Sciences
Project Summary
Signals that cells receive over time from a small set of pathways (e.g., BMP, Wnt, and TGFβ) shape their fate
and phenotype during development, regeneration, and disease. Despite their central importance, signaling
histories of individual cells are often inaccessible to direct observation, hindering quantitative analysis and
obscuring their connection to eventual cell fate. This challenge is particularly pronounced in mammalian
systems, where limited optical access and the constraints of size and timescale often render live imaging
impractical. To address this issue, we have developed an approach to reconstruct the history of signaling
activity in single cells based on endpoint fluorescence images. This is achieved by regulating CRISPR base
editors to generate mutations in engineered target sites at rates proportional to the signal of interest. These
mutations create a heritable record of signaling activity in the genome, which can be read out at a later time,
together with the gene expression profile of the cells. Using this approach, we demonstrated that cells retain a
memory of their past response level to BMP signaling for up to 18 days, providing a mechanism for long-term
interactions between signals that can facilitate coordination of developmental processes over time.
In this proposal, we will expand the scope and utility of our signal recording approach by extending its dynamic
range to capture the broad spectrum of in vivo signal intensities and enabling simultaneous recording of the
sequence and timing of two signaling pathways. We will also engineer mouse embryonic stem cells to record
three key developmental pathways: BMP, Wnt, and Nodal. This will allow us to generate stem cell-derived
embryo models and chimeric embryos to link cell fate and spatial organization at the onset of organogenesis
with signaling activity at different time windows earlier in development. Additionally, we will investigate
mechanisms that enable long-term changes in BMP responsiveness following an initial stimulation, without
requiring differentiation. We will then test whether similar mechanisms exist in Wnt and Nodal pathways and
assess their role in mediating long-term crosstalk between pathways. To achieve these goals, we will take an
interdisciplinary approach combining gene editing, quantitative imaging, epigenomic assays, computational
analysis, and generation of developmental models. The proposed goals build on my prior publications, recent
preliminary data from our lab, and collaborations I have established since launching my lab.
This research program will substantially advance the state of the art in molecular recording, transforming it into
a technology that can be used in vivo, in mammalian systems to drive biological discovery. Our long term vision
is to identify how signaling history controls cellular decision making during development, and how instructions
that cells receive are coordinated over time to produce tissues with the correct number, types, and spatial
arrangement of cells. Ultimately, this knowledge will inform strategies for tissue engineering, and open new
avenues for understanding and treating diseases driven by dysregulated signaling.
Up to $433K
health research