A multi-step transcriptional cascade underlies vascular regeneration in vivo View Full Text


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Article Info

DATE

2018-04-03

AUTHORS

Aditya S. Shirali, Milagros C. Romay, Austin I. McDonald, Trent Su, Michelle E. Steel, M. Luisa Iruela-Arispe

ABSTRACT

The molecular mechanisms underlying vascular regeneration and repair are largely unknown. To gain insight into this process, we developed a method of intima denudation, characterized the progression of endothelial healing, and performed transcriptome analysis over time. Next-generation RNA sequencing (RNAseq) provided a quantitative and unbiased gene expression profile during in vivo regeneration following denudation injury. Our data indicate that shortly after injury, cells immediately adjacent to the wound mount a robust and rapid response with upregulation of genes like Jun, Fos, Myc, as well as cell adhesion genes. This was quickly followed by a wave of proliferative genes. After completion of endothelial healing a vigorous array of extracellular matrix transcripts were upregulated. Gene ontology enrichment and protein network analysis were used to identify transcriptional profiles over time. Further data mining revealed four distinct stages of regeneration: shock, proliferation, acclimation, and maturation. The transcriptional signature of those stages provides insight into the regenerative machinery responsible for arterial repair under normal physiologic conditions. More... »

PAGES

5430

References to SciGraph publications

  • 2001-01-01. Stretch-mediated Activation of Selective MAPK Subtypes and Potentiation of AP-1 Binding in Human Osteoblastic Cells in MOLECULAR MEDICINE
  • 2012-05-22. The importance of the endothelium in atherothrombosis and coronary stenting in NATURE REVIEWS CARDIOLOGY
  • 2017-02-27. A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus in SCIENTIFIC REPORTS
  • 2016-07-27. Mechanisms and regulation of endothelial VEGF receptor signalling in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2011-08-23. Molecular control of endothelial cell behaviour during blood vessel morphogenesis in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2015-01-29. Orchestrating high-throughput genomic analysis with Bioconductor in NATURE METHODS
  • 2008-12-18. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources in NATURE PROTOCOLS
  • 2016-12-08. RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery in SCIENTIFIC REPORTS
  • 2016-08-18. Mechanosensing by the α6-integrin confers an invasive fibroblast phenotype and mediates lung fibrosis in NATURE COMMUNICATIONS
  • 2018-01-31. Multiplexed Detection and Quantitation of Extracellular Vesicle RNA Expression Using NanoString in EXTRACELLULAR RNA
  • 2010-09-26. Endothelial cells dynamically compete for the tip cell position during angiogenic sprouting in NATURE CELL BIOLOGY
  • 2014-12-05. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 in GENOME BIOLOGY
  • 2012-04-15. Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia in NATURE
  • 2005-12-14. Angiogenesis in life, disease and medicine in NATURE
  • 2003-11. AP-1: a double-edged sword in tumorigenesis in NATURE REVIEWS CANCER
  • 2010-06-27. Actin and serum response factor transduce physical cues from the microenvironment to regulate epidermal stem cell fate decisions in NATURE CELL BIOLOGY
  • 2011-05-18. Molecular mechanisms and clinical applications of angiogenesis in NATURE
  • 2015-03-09. HISAT: a fast spliced aligner with low memory requirements in NATURE METHODS
  • Identifiers

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