Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues

  1. Andrew W DeVilbiss
  2. Zhiyu Zhao
  3. Misty S Martin-Sandoval
  4. Jessalyn M Ubellacker
  5. Alpaslan Tasdogan
  6. Michalis Agathocleous
  7. Thomas P Mathews  Is a corresponding author
  8. Sean J Morrison  Is a corresponding author
  1. University of Texas Southwestern Medical Center, United States
  2. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, United States

Abstract

Little is known about the metabolic regulation of rare cell populations because most metabolites are hard to detect in small numbers of cells. We previously described a method for metabolomic profiling of flow cytometrically-isolated hematopoietic stem cells (HSCs) that detects 60 metabolites in 10,000 cells (Agathocleous et al., 2017). Here we describe a new method involving hydrophilic liquid interaction chromatography and high-sensitivity orbitrap mass spectrometry that detected 160 metabolites in 10,000 HSCs, including many more glycolytic and lipid intermediates. We improved chromatographic separation, increased mass resolution, minimized ion suppression, and eliminated sample drying. Most metabolite levels did not significantly change during cell isolation. Mouse HSCs exhibited increased glycerophospholipids relative to bone marrow cells and methotrexate treatment altered purine biosynthesis. Circulating human melanoma cells were depleted for purine intermediates relative to subcutaneous tumors, suggesting decreased purine synthesis during metastasis. These methods facilitate the routine metabolomic analysis of rare cells from tissues.

Data availability

All data generated or analyzed during this study are included in the manuscript and the source data files.

Article and author information

Author details

  1. Andrew W DeVilbiss

    Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9739-2543
  2. Zhiyu Zhao

    Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6308-6997
  3. Misty S Martin-Sandoval

    Children's Medical Center Research Institute at UT Southwestern, Department of Pediatrics, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
  4. Jessalyn M Ubellacker

    Children's Medical Center Research Institute at UT Southwestern, Department of Pediatrics, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
  5. Alpaslan Tasdogan

    Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
  6. Michalis Agathocleous

    Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
  7. Thomas P Mathews

    Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    thomas.mathews@UTSouthwestern.edu
    Competing interests
    No competing interests declared.
  8. Sean J Morrison

    Children's Medical Center Research Institute, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    sean.morrison@utsouthwestern.edu
    Competing interests
    Sean J Morrison, advisor for Frequency Therapeutics and Protein Fluidics as well as a stockholder in G1 Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1587-8329

Funding

Howard Hughes Medical Institute

  • Thomas P Mathews
  • Sean J Morrison

National Institutes of Health

  • Sean J Morrison

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mouse experiments complied with all relevant ethical regulations and were performed according to protocols approved by the Institutional Animal Care and Use Committee at the University of Texas Southwestern Medical Center (protocols 2016-101360 and 2019-102632).

Reviewing Editor

  1. Matthew G Vander Heiden, Massachusetts Institute of Technology, United States

Publication history

  1. Received: August 11, 2020
  2. Accepted: January 19, 2021
  3. Accepted Manuscript published: January 20, 2021 (version 1)
  4. Version of Record published: January 29, 2021 (version 2)

Copyright

© 2021, DeVilbiss et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,743
    Page views
  • 529
    Downloads
  • 16
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Andrew W DeVilbiss
  2. Zhiyu Zhao
  3. Misty S Martin-Sandoval
  4. Jessalyn M Ubellacker
  5. Alpaslan Tasdogan
  6. Michalis Agathocleous
  7. Thomas P Mathews
  8. Sean J Morrison
(2021)
Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
eLife 10:e61980.
https://doi.org/10.7554/eLife.61980

Further reading

    1. Neuroscience
    2. Stem Cells and Regenerative Medicine
    Bilal Cakir, In-Hyun Park
    Insight

    Fusing brain organoids with blood vessel organoids leads to the incorporation of non-neural endothelial cells and microglia into the brain organoids.

    1. Computational and Systems Biology
    2. Stem Cells and Regenerative Medicine
    Genki N Kanda et al.
    Research Article

    Induced differentiation is one of the most experience- and skill-dependent experimental processes in regenerative medicine, and establishing optimal conditions often takes years. We developed a robotic AI system with a batch Bayesian optimization algorithm that autonomously induces the differentiation of induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells. From 200 million possible parameter combinations, the system performed cell culture in 143 different conditions in 111 days, resulting in 88% better iPSC-RPE production than that obtained by the pre-optimized culture in terms of the pigmentation scores. Our work demonstrates that the use of autonomous robotic AI systems drastically accelerates systematic and unbiased exploration of experimental search space, suggesting immense use in medicine and research.