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The in vivo endothelial cell translatome is highly heterogeneous across vascular beds

Cleuren, Audrey C. A., van der Ent, Martijn A., Jiang, Hui, Hunker, Kristina L., Yee, Andrew, Siemieniak, David R., Molema, Grietje, Aird, William C., Ganesh, Santhi K., Ginsburg, David·2019·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1912409116

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Abstract

Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.

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Metadata

Authors
Cleuren, A. C. A., van der Ent, M. A., Jiang, H., Hunker, K. L., Yee, A., Siemieniak, D. R., Molema, G., Aird, W. C., Ganesh, S. K., & Ginsburg, D.
Affiliations
  • Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109;
  • Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109;
  • Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109;
  • Department of Pathology and Medical Biology, University of Groningen, 9700 RB Groningen, The Netherlands;
  • Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA 02215;
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2019-11-11
Volume
116
Issue
47
Pages
23618-23624
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.1912409116
Cited by
152
References
11
Language
en
Licence
www.pnas.org/site/aboutpnas/licenses.xhtml (vor, 182 d)
Funders
  • HHS | NIH | National Heart, Lung, and Blood Institute (R35HL135793, R01HL122684)
  • American Heart Association (16POST27770093)
  • Howard Hughes Medical Institute (No number)

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