# Sub-Cellular Mass Spectrometry Discoveries: Metabolic Encoding of the Embryonic Body Plan

> **NIH NIH R35** · UNIV OF MARYLAND, COLLEGE PARK · 2024 · $437,836

## Abstract

Abstract
A critical process for early development of the vertebrate embryo is induction of the three primary germ layers.
Knowledge of the molecules that are produced in each embryonic cell is essential to understanding their
function to pattern the embryonic body. Decades of innovative cell biological and embryological studies,
assessment of function one gene at a time, and recently deep transcriptomics profiling via next-generation
sequencing have exposed the developmental roles of important genes, transcripts, and some proteins. As a
result, scientists have defined the spatial and temporal changes of mRNAs and abundant proteins, and some
serendipitously identified metabolites of importance, such as folate assisting in closure of the neural tube.
However, it has been technologically impossible to utilize high-resolution mass spectrometry (HRMS), the gold
standard technology for proteomics and metabolomics (`omics), to study hundreds of metabolites and
thousands proteins in single embryonic cells in the vertebrate embryo. Further, in developing systems, a
complex correlation between gene transcription and translation as well as posttranslational modifications
complicate the use of mRNA information to approximate protein and metabolite levels. Without the availability
of single-cell HRMS as a routine laboratory tool or other technologies capable of deep metabolomics and
proteomics, scientists at present lack insights into metabolic processes that contribute to early embryonic
patterning. The research program proposed here fills this enormous knowledge and technological gap by
utilizing ultrahigh-sensitivity HRMS platforms that were custom-designed, custom-built, and validated in the
vertebrate frog (Xenopus laevis) embryo, a popular model in cell/developmental biology, to understand
noncanonical metabolomic processes that control formation of the germ layers. Most recently, single-cell
HRMS in X. laevis has discovered metabolites that are capable of (i) altering the normal cell fates of embryonic
cells, (ii) communicating between blastomeres, and (iii) affecting the whole-organismal performance of the
resulting tadpole. These findings have shed light on a gap in our basic knowledge of molecules participating in
the successful induction of the germ layers. This research program will determine roles that metabolites play in
patterning the embryonic body plan. This work will integrate classical embryological manipulations, cell-fate
tracking, and fluorescent microscopy with new-generation quantitative mass spectrometry capable of
subcellular sensitivity to characterize how targeted metabolic reactions impact reproducible tissue fates in the
X. laevis embryo. Because these molecular processes are highly conserved across vertebrates, the data
collected from Xenopus are likely to have high relevance to human development. This interdisciplinary
research program will help discover metabolic mechanisms governing cell differentiation and embryogenesis.

## Key facts

- **NIH application ID:** 10765477
- **Project number:** 2R35GM124755-07
- **Recipient organization:** UNIV OF MARYLAND, COLLEGE PARK
- **Principal Investigator:** Peter Nemes
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $437,836
- **Award type:** 2
- **Project period:** 2017-09-01 → 2029-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10765477

## Citation

> US National Institutes of Health, RePORTER application 10765477, Sub-Cellular Mass Spectrometry Discoveries: Metabolic Encoding of the Embryonic Body Plan (2R35GM124755-07). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10765477. Licensed CC0.

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