# Systems Analysis of cell type differentiation in Xenopus development

> **NIH NIH R01** · HARVARD MEDICAL SCHOOL · 2022 · $315,084

## Abstract

Summary
The pathways involved in embryonic development have been a rich resource for understanding disease in
adults, as well as being critically important in tracing the effects of genetic lesions and environmental poisons
in the fetus. Frog embryos have been particularly useful due to the large size of the frog egg and embryo. New
tools we developed for measuring the expression of RNA at a single-cell level, and advances in protein and
phosphopeptide measurement technologies, offer hope for dramatic progress in understanding how signals
involved in the maturation of the embryo direct individual cells to adopt specific fates. Our first goal is to define
cell types using single-cell transcriptomics, and to define the lineages that result in specific cell types using high
resolution temporal mappings. Targeted transcriptomics and proteomics of important molecules involved in
specifying cell fate, such as transcription factors, will provide an index of the levels of signaling activity in each
individual cell. This will result in an unprecedentedly detailed molecular picture of the factors involved in
producing the phenotypes, and their interconversions from the early cleavage stage to the middle of
organogenesis.
The Xenopus model system allows us to dissect out portions of the early embryo that differentiate to ectoderm
if not disturbed, called the animal cap. In the context of the embryo the cells in the animal cap receive a
number of developmental signals, including Nodal, BMP, and Wnt. Combinations of these three signals (in
different proportions) are capable of generating many of the major tissues. We will expose animal caps to a
matrix of these three signals and trace the differentiation pathways that result, using single-cell RNA
sequencing. This study of the molecular roots of differentiation decisions will be used to develop a
mathematical approach, based on machine learning, to predicting the results of an attempted perturbation of
the development of Xenopus. We will ask whether cell types are carefully specified by tightly controlled
combinations of ligands or whether there are default states that are hard to escape from ("basins of
attraction"), that therefore form the majority of embryonic cell types. The answer to this question is central to
our understanding of how the Xenopus embryo reliably develops into a frog, and will accelerate efforts to
create computational methods to predict the behavior of other biological pathways such as those involved in
cancer.

## Key facts

- **NIH application ID:** 10625740
- **Project number:** 3R01HD073104-10S1
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** MARC Wallace KIRSCHNER
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $315,084
- **Award type:** 3
- **Project period:** 2012-09-01 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10625740

## Citation

> US National Institutes of Health, RePORTER application 10625740, Systems Analysis of cell type differentiation in Xenopus development (3R01HD073104-10S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10625740. Licensed CC0.

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