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Cell Mol Gastroenterol Hepatol. 2018 May 16;6(2):181-198. doi: 10.1016/j.jcmgh.2018.05.002. eCollection 2018.

E47 Governs the MYC-CDKN1B/p27KIP1-RB Network to Growth Arrest PDA Cells Independent of CDKN2A/p16INK4A and Wild-Type p53.

Author information

Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
Center for Computational Biology and Bioinformatics, School of Medicine.
Department of Surgery, Division of Surgical Oncology, Moores Cancer Center.
Genomics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
Department of Pediatrics, University of California San Diego, La Jolla, California.


Background & Aims:

Oncogenic mutations in KRAS, coupled with inactivation of p53, CDKN2A/p16INK4A, and SMAD4, drive progression of pancreatic ductal adenocarcinoma (PDA). Overexpression of MYC and deregulation of retinoblastoma (RB) further promote cell proliferation and make identifying a means to therapeutically alter cell-cycle control pathways in PDA a significant challenge. We previously showed that the basic helix-loop-helix transcription factor E47 induced stable growth arrest in PDA cells in vitro and in vivo. Here, we identified molecular mechanisms that underlie E47-induced growth arrest in low-passage, patient-derived primary and established PDA cell lines.


RNA sequencing was used to profile E47-dependent transcriptomes in 5 PDA cell lines. Gene Ontology analysis identified cell-cycle control as the most altered pathway. Small interfering RNA/short hairpin RNA knockdown, small-molecule inhibitors, and viral expression were used to examine the function of E47-dependent genes in cell-cycle arrest. Cell morphology, expression of molecular markers, and senescence-associated β-galactosidase activity assays identified cellular senescence.


E47 uniformly inhibited PDA cell-cycle progression by decreasing expression of MYC, increasing the level of CDKN1B/p27KIP1, and restoring RB tumor-suppressor function. The molecular mechanisms by which E47 elicited these changes included altering both RNA transcript levels and protein stability of MYC and CDKN1B/p27KIP1. At the cellular level, E47 elicited a senescence-like phenotype characterized by increased senescence-associated β-galactosidase activity and altered expression of senescence markers.


E47 governs a highly conserved network of cell-cycle control genes, including MYC, CDKN1B/p27KIP1, and RB, which can induce a senescence-like program in PDA cells that lack CDKN2A/p16INK4A and wild-type p53. RNA sequencing data are available at the National Center for Biotechnology Information GEO at; accession number: GSE100327.


CDK, cyclin-dependent kinase; CDKN1B/p27KIP1, CDKN1B/p27Kinase Inhibitory Protein 1; CDKN2A/p16INK4A, CDKN2A/p16Inhibitor of CDK 4A; CEBP-α, CCAAT/enhancer binding protein alpha; CENP-A, centromere protein A; CIP, Cyclin-Dependent Kinase Inhibitor 1; Cell Cycle; DDR, DNA damage response; ERK, extracellular signal–regulated kinase; GO, Gene Ontology; INK, Inhibitor of CDK; KIP, Kinase Inhibitory Protein; MSCV, murine stem cell virus; OIS, oncogene-induced senescence; PCR, polymerase chain reaction; PDA, pancreatic ductal adenocarcinoma; Pancreatic Ductal Adenocarcinoma; RB, retinoblastoma; RNA-seq, RNA sequencing; SA-βgal, senescence-associated β-galactosidase; SKP, S-phase Kinase-associated; Senescence; bHLH; bHLH, basic helix-loop-helix; lfdr, local false discovery rate; mRNA, messenger RNA; shRB, short hairpin RNA directed against RB; shRNA, short hairpin RNA; si-p27, small interfering RNA directed against p27

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