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Multi-omics characterization of mesenchymal stem/stromal cells for the identification of putative critical quality attributes

Ty S. Maughon, Xunan Shen, Danning Huang, Adeola O Adebayo Michael, William A. Shockey, Seth H. Andrews, Jon M. McRae III, Manu O Platt, Facundo M. Fernández, Arthur S. Edison, Steven L. Stice, View ORCID ProfileRoss A. Marklein
doi: https://doi.org/10.1101/2021.05.10.440010
Ty S. Maughon
1School of Chemical, Materials, and Biomedical Engineering, University of Georgia
2Regenerative Bioscience Center, University of Georgia
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Xunan Shen
4Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia
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Danning Huang
5School of Chemistry and Biochemistry, Georgia Institute of Technology
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Adeola O Adebayo Michael
6Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology
7Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology
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William A. Shockey
6Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology
7Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology
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Seth H. Andrews
1School of Chemical, Materials, and Biomedical Engineering, University of Georgia
2Regenerative Bioscience Center, University of Georgia
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Jon M. McRae III
2Regenerative Bioscience Center, University of Georgia
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Manu O Platt
6Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology
7Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology
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Facundo M. Fernández
5School of Chemistry and Biochemistry, Georgia Institute of Technology
7Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology
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Arthur S. Edison
4Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia
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Steven L. Stice
2Regenerative Bioscience Center, University of Georgia
3Department of Animal and Dairy Sciences, University of Georgia
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  • For correspondence: ROSS.MARKLEIN@uga.edu sstice@uga.edu
Ross A. Marklein
1School of Chemical, Materials, and Biomedical Engineering, University of Georgia
2Regenerative Bioscience Center, University of Georgia
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  • ORCID record for Ross A. Marklein
  • For correspondence: ROSS.MARKLEIN@uga.edu sstice@uga.edu
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Abstract

Background Mesenchymal stromal cells (MSCs) have shown great promise in the field of regenerative medicine as many studies have shown that MSCs possess immunomodulatory function. Despite this promise, no MSC therapies have been granted licensure from the FDA. This lack of successful clinical translation is due in part to MSC heterogeneity and a lack of critical quality attributes (CQAs). While MSC Indoleamine 2,3-dioxygnease (IDO) activity has been shown to correlate with MSC function, multiple CQAs may be needed to better predict MSC function.

Methods Three MSC lines (two bone marrow, one iPSC) were expanded to three passages. At the time of harvest for each passage, cell pellets were collected for nuclear magnetic resonance (NMR) and ultra-performance liquid chromatography mass spectrometry (UPLC-MS), and media was collected for cytokine profiling. Harvested cells were also cryopreserved for assessing function using T cell proliferation and IDO activity assays. Linear regression was performed on functional and multiomics data to reduce the number of important features, and partial least squares regression (PLSR) was used to obtain putative CQAs based on variable importance in projection (VIP) scores.

Results Significant functional heterogeneity (in terms of T cell suppression and IDO activity) was observed between the three MSC lines, as well as donor-dependent differences based on passage. Omics characterization revealed distinct differences between cell lines using principal component analysis (PCA). Cell lines separated along principal component 1 based on tissue source (bone marrow vs. iPSC-derived) for NMR, MS, and cytokine profiles. PLSR modeling of important features predicts MSC functional capacity with NMR (R2=0.86), MS (R2=0.83), cytokines (R2=0.70), and a combination of all features (R2=0.88).

Discussion The work described here provides a platform for identifying putative CQAs for predicting MSC functional capacity using PLSR modeling that could be used as release criteria and guide future manufacturing strategies for MSCs and other cell therapies.

Competing Interest Statement

RoosterBio provided a discount for the bone marrow cells.

Footnotes

  • https://www.metabolomicsworkbench.org/

  • Abbreviations

    MSC
    Mesenchymal stem/stromal cells
    CQA
    critical quality attributes
    PBMC
    peripheral blood mononuclear cell
    ISCT
    The International Society for Cell and Gene Therapy
    IDO
    indoleamine 2,3-dioxygenase
    OXPHOS
    oxidative phosphorylation
    NMR
    nuclear magnetic resonance
    MS
    mass spectrometry
    GC
    gas chromatography
    UPLC
    ultra-performance liquid chromatography
    PLSR
    partial least squares regression
    VIP
    variable importance projection
    IFN-γ
    interferon gamma
    1D-NOESY PR
    one dimensional nuclear Overhauser enhancement spectroscopy with water suppression
    COW
    correlation optimized wrapping
    PQN
    probabilistic quotient normalization
    HSQC
    heteronuclear single quantum coherence
    HSQC-TOCSY
    HSQC-total correlated spectroscopy
    HILIC
    hydrophilic interaction chromatography
    DDA
    data-dependent acquisition
    NCE
    normalized collision energy
    PCA
    principal component analysis
    PCs
    phosphatidylcholines
    ukNMR-n
    unknown NMR metabolite n
    ukM-n
    unknown MS metabolite n
    EpdSCs
    epidermal stem cells
    CAR-T
    chimeric antigen receptor T-cell
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Multi-omics characterization of mesenchymal stem/stromal cells for the identification of putative critical quality attributes
    Ty S. Maughon, Xunan Shen, Danning Huang, Adeola O Adebayo Michael, William A. Shockey, Seth H. Andrews, Jon M. McRae III, Manu O Platt, Facundo M. Fernández, Arthur S. Edison, Steven L. Stice, Ross A. Marklein
    bioRxiv 2021.05.10.440010; doi: https://doi.org/10.1101/2021.05.10.440010
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    Multi-omics characterization of mesenchymal stem/stromal cells for the identification of putative critical quality attributes
    Ty S. Maughon, Xunan Shen, Danning Huang, Adeola O Adebayo Michael, William A. Shockey, Seth H. Andrews, Jon M. McRae III, Manu O Platt, Facundo M. Fernández, Arthur S. Edison, Steven L. Stice, Ross A. Marklein
    bioRxiv 2021.05.10.440010; doi: https://doi.org/10.1101/2021.05.10.440010

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