Single-cell RNA-Seq of bone marrow-derived mesenchymal stem cells reveals unique profiles of lineage priming

Brian T. Freeman, Jangwook P. Jung, Brenda M. Ogle

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49 Scopus citations


The plasticity and immunomodulatory capacity of mesenchymal stem cells (MSCs) have spurred clinical use in recent years. However, clinical outcomes vary and many ascribe inconsistency to the tissue source of MSCs. Yet unconsidered is the extent of heterogeneity of individual MSCs from a given tissue source with respect to differentiation potential and immune regulatory function. Here we use single-cell RNA-seq to assess the transcriptional diversity of murine mesenchymal stem cells derived from bone marrow. We found genes associated with MSC multipotency were expressed at a high level and with consistency between individual cells. However, genes associated with osteogenic, chondrogenic, adipogenic, neurogenic and vascular smooth muscle differentiation were expressed at widely varying levels between individual cells. Further, certain genes associated with immunomodulation were also inconsistent between individual cells. Differences could not be ascribed to cycles of proliferation, culture bias or other cellular process, which might alter transcript expression in a regular or cyclic pattern. These results support and extend the concept of lineage priming of MSCs and emphasize caution for in vivo or clinical use of MSCs, even when immunomodulation is the goal, since multiple mesodermal (and even perhaps ectodermal) outcomes are a possibility. Purification might enable shifting of the probability of a certain outcome, but is unlikely to remove multilineage potential altogether.

Original languageEnglish (US)
Article numbere0136199.
JournalPloS one
Issue number9
StatePublished - Sep 9 2015

Bibliographical note

Funding Information:
We thank Kenneth Beckman, Adam Hauge and Jerry Daniel of the University of Minnesota Genomics Center for technical assistance with the single-cell capture, cDNA preparation and RNA-seq, and Josh Baller and John Garbe of the Minnesota Supercomputing Institute at the University of Minnesota-Twin Cities for assistance with analysis of RNA-seq data. The present study was supported by the National Institutes of Health (HL089679), National Science Foundation Graduate Research Fellowship Program (NSF-GRFP 2010105691), National Science Foundation (CAREER, award 0844537), University of Minnesota Genomics Center, New Investigator Award.

Publisher Copyright:
© 2015 Freeman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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