A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence

BMC Genomics. 2019 Apr 15;20(1):290. doi: 10.1186/s12864-019-5653-x.


Background: Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or therapy-induced senescence has been alternatively proposed to contribute to therapeutic efficacy or resistance. Toward better understanding this cell state, we sought to define the core transcriptome of accelerated senescence in cancer cells.

Results: We examined senescence induced by ionizing irradiation or ectopic overexpression of the stoichiometric cyclin-dependent kinase (CDK) inhibitor p21CIP/WAF1/SDI1 in the human breast cancer cell line MCF7. While radiation produces a strong DNA damage response, ectopic expression of p21 arrests cell cycle progression independently of DNA damage. Both conditions promoted senescence within 5 days. Microarray analysis revealed 378 up- and 391 down-regulated genes that were shared between the two conditions, representing a candidate signature. Systems analysis of the shared differentially expressed genes (DEGs) revealed strong signals for cell cycle control and DNA damage response pathways and predicted multiple upstream regulators previously linked to senescence. Querying the shared DEGs against the Connectivity Map (cmap) database of transcriptional responses to small molecules yielded 20 compounds that induce a similar gene expression pattern in MCF7 cells. Of 16 agents evaluated, six induced senescence on their own. Of these, the selective estrogen receptor degrader fulvestrant and the histone acetyltransferase inhibitor vorinostat did so without causing chromosomal damage.

Conclusions: Using a systems biology approach with experimental validation, we have defined a core gene expression signature for therapy-induced senescence.

Keywords: Connectivity map analysis; DNA damage foci; Differential expression genes; Radiation-induced senescence; Small molecule inhibitors; Transcriptome analysis; Upstream regulator factors; p21-induced senescence.

MeSH terms

  • Cellular Senescence / drug effects*
  • Cellular Senescence / genetics*
  • Computational Biology / methods*
  • Humans
  • MCF-7 Cells
  • Small Molecule Libraries / pharmacology*
  • Transcriptome / drug effects*
  • p21-Activated Kinases / metabolism


  • Small Molecule Libraries
  • p21-Activated Kinases