# Chemical tools for developmental biology

> **NIH NIH R35** · STANFORD UNIVERSITY · 2022 · $775,554

## Abstract

Tissue morphogenesis and regeneration requires dynamic, robust control of cell proliferation,
differentiation, and migration. To coordinate these complex cell behaviors, developmental signaling pathways
are actuated with spatiotemporal precision, and their dysregulation can lead to congenital birth defects or
tumorigenesis later on in life. While developmental biologists have largely relied on genetic tools to deconstruct
these processes, our laboratory has taken a different approach. Over the past five years, we have explored
how chemical technologies and high-throughput biology can deepen our understanding of developmental
signaling and tissue patterning. Over the past five years, we have invented caged morpholino oligonucleotides
that can be activated by light or enzymatically triggered, and we have used these chemical tools to gain new
insights into notochord, somite, and medial floor plate development. We established methods for the
ultrasensitive imaging of lanthanide-based probes, allowing their unique photophysical properties to be fully
exploited for autofluorescence-free in vivo imaging. We have also discovered novel regulators of the Hedgehog
pathway, including ARHGAP36, a non-canonical GLI transcription factor activator and oncogene, and the first
specific small-molecule inhibitors of cytoplasmic dyneins.
 We now seek to build upon these accomplishments and push the boundaries of in vivo chemical biology,
focusing on the photochemistry of metal ions, synthetic compounds, and proteins. We envision that
developmental biology would benefit from new optically controlled technologies that match the cellular
resolution and rapid kinetics of patterning mechanisms, including both graded and switch-like responses.
Imaging modalities that enable the detection of RNAs, proteins, and their activities at physiological
concentrations would be equally transformative. Our research plans for the next five years include the
synthesis of photoactivatable morpholinos with greater dynamic and spectral range, directed evolution of
optogenetic regulators for key developmental signaling pathways, and design of lanthanide-based tools for
imaging biological molecules in whole organisms. We will apply these technologies in zebrafish models, taking
advantage of their optical transparency and amenability to chemical and genetic manipulations. Our long-term
goal is to use these new experimental capabilities to perturb and observe in vivo biology in unprecedented
ways, changing how we study and understand the molecular mechanisms that give rise to multicellular form.

## Key facts

- **NIH application ID:** 10369652
- **Project number:** 5R35GM127030-05
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** JAMES K CHEN
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $775,554
- **Award type:** 5
- **Project period:** 2018-04-01 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10369652

## Citation

> US National Institutes of Health, RePORTER application 10369652, Chemical tools for developmental biology (5R35GM127030-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10369652. Licensed CC0.

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