# Single-cell Metabolomics and Proteomics: The Missing Link to Understanding Vertebrate Embryonic Patterning

> **NIH NIH R35** · UNIV OF MARYLAND, COLLEGE PARK · 2021 · $366,348

## Abstract

Abstract
Understanding embryonic development requires knowledge of all the molecules produced as the zygote
differentiates into the three primary germ layers of the embryo. Four decades of innovative embryological
manipulations, testing of gene functions one gene at a time, and recently, Next-Generation Sequencing have
identified multiple transcripts and abundant proteins that are essential to the patterning of the vertebrate
embryo. However, very little is known about the total array of proteins and their post-translational modifications
that contribute to the formation of the germ layers, and next to nothing is known about the contribution of small
molecules (called metabolites) to these processes. To date, systems biology has defined the spatial and
temporal changes of mRNAs, abundant proteins, and metabolites in the whole embryo, but it has been
technologically impossible to utilize high-resolution mass spectrometry (HRMS), the gold standard technology
for small molecules, to study hundreds-to-thousands of metabolites and proteins in single embryonic cells in
the vertebrate embryo. The proposed research program fills this enormous knowledge and technological gap
by utilizing novel single-cell mass spectrometry technologies to understand cell molecular processes that
contribute to the formation of the three germ layers required for the successful patterning of the vertebrate frog
(Xenopus laevis) embryo, a favorite model in cell/developmental biology. Most recently, single-cell mass
spectrometry discovered metabolites capable of altering the normal cell fates of embryonic cells, suggesting
that the complete molecular players are not yet fully identified or understood for germ layer induction. The
proposed research program will determine this missing link in the understanding of molecular mechanisms
governing vertebrate development. This work will integrate quantitative single-cell mass spectrometry, cell fate
tracking, and gene knock-down experiments to determine how a targeted set of small-molecular reactions
impact the formation of signaling centers required for dorsal axis specification. The outcomes of this
interdisciplinary approach will help illuminate the role of the proteome and metabolome for the establishment of
these important precursors. Because these molecular processes are highly conserved across vertebrates, the
data collected from Xenopus are likely to have high relevance to human structural birth defects. The new
biochemical information that will be obtained in individual embryonic cells and their progeny (cell lineage) at
several critical developmental time points will also advance other research fields that involve cell differentiation
(e.g., of stem cells) and the developmental origins of adult disease.

## Key facts

- **NIH application ID:** 10247791
- **Project number:** 5R35GM124755-06
- **Recipient organization:** UNIV OF MARYLAND, COLLEGE PARK
- **Principal Investigator:** Peter Nemes
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $366,348
- **Award type:** 5
- **Project period:** 2017-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10247791

## Citation

> US National Institutes of Health, RePORTER application 10247791, Single-cell Metabolomics and Proteomics: The Missing Link to Understanding Vertebrate Embryonic Patterning (5R35GM124755-06). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10247791. Licensed CC0.

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